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Iqbal Z, Fauzia Farheen Zofair S, Ahmed S, Sharma M, Younus H, Mahmood R. Interaction of plant phenol vanillin with human hemoglobin: A spectroscopic and molecular docking study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124831. [PMID: 39024790 DOI: 10.1016/j.saa.2024.124831] [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: 11/15/2023] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/20/2024]
Abstract
Vanillin is a phenolic aldehyde widely used as a flavouring agent in the food industry. Vanillin has many health benefits and has gained attention in pharmacological industries also, due to its antioxidant properties and non-toxic nature. The interaction of vanillin with human hemoglobin (hHb), an abundant tetrameric heme protein, was investigated by several spectroscopic techniques and molecular modeling methods. UV-visible spectra showed that the binding of vanillin to hHb induces structural changes due to alterations in the micro-environment of hHb. Vanillin quenches the intrinsic fluorescence of hHb by the dynamic mechanism, which was confirmed by both temperature dependent and time resolved fluorescence studies. Vanillin binds spontaneously to hHb at a single site and the binding is stabilized by hydrogen bonds and hydrophobic interactions. The circular dichroism spectra showed that the binding of vanillin altered the secondary structure of hHb due to change in its alpha-helical content. Molecular docking identified the amino acids of hHb involved in binding to vanillin and also that the free energy change of the binding reaction is -5.5 kcal/mol. Thus, our results indicate that vanillin binds spontaneously to hHb at a single site and alters its secondary structure. This will help in understanding the potential use of vanillin and related antioxidants as therapeutic agents in various hematological disorders.
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Affiliation(s)
- Zarmin Iqbal
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Syeda Fauzia Farheen Zofair
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Shahbaz Ahmed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Monika Sharma
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Hina Younus
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Riaz Mahmood
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, UP, India.
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Fatima M, Nabi F, Khan RH, Naeem A. Investigating the binding interaction of quinoline yellow with bovine serum albumin and anti-amyloidogenic behavior of ferulic acid on QY-induced BSA fibrils. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124076. [PMID: 38442614 DOI: 10.1016/j.saa.2024.124076] [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: 08/29/2023] [Revised: 01/30/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024]
Abstract
Protein aggregation induces profound changes in the structure along with the conformation of the protein, and is responsible for the pathogenesis of a number of neurodegenerative conditions such as Huntington's, Creutzfeldt-Jacob, Type II diabetes mellitus, Alzheimer's, etc. Numerous multi-spectroscopic approaches and in-silico experiments were utilized to investigate BSA's biomolecular interaction and aggregation in the presence of quinoline yellow. The present research investigation evaluated the interaction of BSA with the food colorant (QY) at two different pH (7.4 and 2.0). The development of the BSA-QY complex was established with UV visible and fluorescence spectroscopy. The quenching of fluorescence upon the interaction of BSA with QY revealed the static nature of quenching mechanism. The Kb value obtained from our result is 4. 54 × 10-4 M-1. The results from the competitive site marker study infer that quinoline yellow is binding with the sub-domain IB of bovine serum albumin, specifically on site III. Three-dimensional fluorescence and synchronous fluorescence spectroscopy were applied for monitoring the alterations in the microenvironment of BSA upon the addition of quinoline yellow. The results from turbidity and RLS studies showed that higher concentrations of QY (80-400 µM) triggered bovine serum albumin (BSA) aggregation at pH 2.0. At pH 7.4, QY couldn't manage to trigger bovine serum albumin aggregation, perhaps because of the repulsion between negatively charged dye (QY) and anionic bovine serum albumin. The results from far-UV CD, Congo Red, and scanning electron microscopy implicate that the QY-induced aggregates exhibit amyloid fibril-like structures. Molecular docking results revealed that hydrophobic interactions, hydrogen bonding, and Pi-Sulfur interactions contribute to QY-induced aggregation of BSA. Further, the amyloid inhibitory potential of ferulic acid (FA), a phenolic acid on QY-induced aggregation of BSA, has also been assessed. The QY-induced amyloid fibrils are FA-soluble, as confirmed by turbidity, RLS, and far-UV CD studies. Far-UV CD results showed that FA retains α helix and inhibits cross β sheet formation when the BSA samples were pre-incubated with increasing concentrations of FA (0-500 µM). Our findings conclude that QY dye successfully stimulates BSA aggregation, but ferulic acid inhibits QY-induced aggregation of BSA. Thus, FA can serve as a therapeutic agent and can help in the treatment of various amyloid-related conditions.
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Affiliation(s)
- Maham Fatima
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, U.P., India.
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Qais FA, Furkan M, Altaf M, Ahmad I, Khan RH. Exploring the mechanism of interaction of glipizide with DNA: Combined in vitro and bioinformatics approach. Int J Biol Macromol 2024; 267:131573. [PMID: 38614188 DOI: 10.1016/j.ijbiomac.2024.131573] [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: 02/19/2024] [Revised: 03/27/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
DNA, vital for biological processes, encodes hereditary data for protein synthesis, shaping cell structure and function. Since revealing its structure, DNA has become a target for various therapeutically vital molecules, spanning antidiabetic to anticancer drugs. These agents engage with DNA-associated proteins, DNA-RNA hybrids, or bind directly to the DNA helix, triggering diverse downstream effects. These interactions disrupt vital enzymes and proteins essential for maintaining cell structure and function. Analysing drug-DNA interactions has significantly advanced our understanding of drug mechanisms. Glipizide, an antidiabetic drug, is known to cause DNA damage in adipocytes. However, its extract mechanism of DNA interaction is unknown. This study delves into the interaction between glipizide and DNA utilizing various biophysical tools and computational technique to gain insights into the interaction mechanism. Analysis of UV-visible and fluorescence data reveals the formation of complex between DNA and glipizide. The binding affinity of glipizide to DNA was of moderate strength. Examination of thermodynamic parameters at different temperatures suggests that the binding was entropically spontaneous and energetically favourable. Various experiments such as thermal melting assays, viscosity measurement, and dye displacement assays confirmed the minor grove nature of binding of glipizide with DNA. Molecular dynamics studies confirmed the glipizide forms stable complex with DNA when simulated by mimicking the physiological conditions. The binding was mainly favoured by hydrogen bonds and glipizide slightly reduced nucleotide fluctuations of DNA. The study deciphers the mechanism of interaction of glipizide with DNA at molecular levels.
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Affiliation(s)
- Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Furkan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Mohammad Altaf
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, 11451 Riyadh, Saudi Arabia
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, UP, India.
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Afzal M, Qais FA, Abduh NA, Christy M, Ayub R, Alarifi A. Identification of bioactive compounds of Zanthoxylum armatum as potential inhibitor of pyruvate kinase M2 (PKM2): Computational and virtual screening approaches. Heliyon 2024; 10:e27361. [PMID: 38495183 PMCID: PMC10943388 DOI: 10.1016/j.heliyon.2024.e27361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
PKM2 (Pyruvate kinase M2) is the isoform of pyruvate kinase which is known to catalyse the last step of glycolysis that is responsible for energy production. This specific isoform is known to be highly expressed in certain cancerous conditions. Considering the role of this protein in various cancer conditions, we used PKM2 as a target protein to identify the potential compounds against this target. In this study, we have examined 96 compounds of Zanthoxylum armatum using an array of computational and in silico tools. The compounds were assessed for toxicity then their anticancer potential was predicted. The virtual screening was done with molecular docking followed by a detailed examination using molecular dynamics simulation. The majority of the compounds showed a higher probability of being antineoplastic. Based on toxicity, predicted anticancer potential, binding affinity, and binding site, three compounds (nevadensin, asarinin, and kaempferol) were selected as hit compounds. The binding energy of these compounds with PKM2 ranged from -7.7 to -8.3 kcal/mol and all hit compounds interact at the active site of the protein. The selected hit compounds formed a stable complex with PKM2 when simulated under physiological conditions. The dynamic analysis showed that these compounds remained attached to the active site till the completion of molecular simulation. MM-PBSA analysis showed that nevadensin exhibited a higher affinity towards PKM2 compared to asarinin and kaempferol. These compounds need to be assessed properties in vivo and in vitro to validate their efficacy.
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Affiliation(s)
- Mohd Afzal
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, UP, 202002, India
| | - Naaser A.Y. Abduh
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Maria Christy
- Department of Energy Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, South Korea
| | - Rashid Ayub
- Department of Science Technology and Innovation, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Abdullah Alarifi
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
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Daksh S, Gond C, Kumar N, Kaur L, Ojha H, Deep S, Datta A. Binding studies of potential amyloid-β inhibiting chalcone derivative with bovine serum albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123362. [PMID: 37774582 DOI: 10.1016/j.saa.2023.123362] [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: 05/28/2023] [Revised: 08/23/2023] [Accepted: 09/04/2023] [Indexed: 10/01/2023]
Abstract
Chalcones (α-phenyl-β-benzoylethylene) and their natural-source derivatives have been investigated for their remarkable biological activities, like neuroprotective, anti-inflammatory, and anti-tumor properties. A triazole chalcone ligand (E)-3-(4-(dimethylamino)phenyl)-1-(4-((1-(2-(4-((E)-3-(4(dimethylamino)phenyl)acryloyl)phenoxy)ethyl)-1H-1,2,3-triazol-4-yl)methoxy)phenyl)prop-2-en-1-one (L1) was synthesized by Cu(I)- catalysed click reaction. The mechanistic properties of L1 for therapy were evaluated by analyzing the binding interactions between L1 and bovine serum albumin (BSA) through photophysical and computational studies. The structural elucidation of ligand L1 was carried out by NMR and mass spectrometry. The Aβ inhibitory activity of L1 was studied by thioflavin T assay and transmission electron microscopy. The biomolecular interaction of L1 with bovine serum albumin was examined through multi-spectroscopic techniques in combination with in silico studies. UV-Visible absorption, fluorescence spectroscopy, circular dichroism, Förster resonance energy transfer, and three-dimensional fluorescence studies confirmed the formation of a BSA-L1 complex. The potential binding sites, mechanism of interactions, and variations in the environment of tyrosine and tryptophan amino acid residues of BSA were assessed at different temperatures. The binding constant for the Static quenching mechanism of intrinsic fluorescence of BSA was of the order of 105 M-1. The esterase enzyme activity assay in the presence of L1 revealed an increase in the protein enzyme activity. Molecular docking studies suggested L1 was predominantly bound to BSA by hydrogen bonds and Van der Waals forces.
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Affiliation(s)
- Shivani Daksh
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Brig S. K. Mazumdar Marg, Delhi 110054, India; Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Chandraprakash Gond
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, Uttar Pradesh, India
| | - Nikhil Kumar
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Brig S. K. Mazumdar Marg, Delhi 110054, India; Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Lajpreet Kaur
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Brig S. K. Mazumdar Marg, Delhi 110054, India
| | - Himanshu Ojha
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Brig S. K. Mazumdar Marg, Delhi 110054, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India.
| | - Anupama Datta
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Brig S. K. Mazumdar Marg, Delhi 110054, India.
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Adamczyk O, Szota M, Rakowski K, Prochownik M, Doveiko D, Chen Y, Jachimska B. Bovine Serum Albumin as a Platform for Designing Biologically Active Nanocarriers-Experimental and Computational Studies. Int J Mol Sci 2023; 25:37. [PMID: 38203208 PMCID: PMC10778598 DOI: 10.3390/ijms25010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Due to the specificity of their structure, protein systems are adapted to carry various ligands. The structure of many proteins potentially allows for two types of immobilization of a therapeutic agent, either on the outer surface of the protein or within the protein structure. The existence of two active sites in BSA's structure, the so-called Sudlow I and II, was confirmed. The conducted research involved determining the effectiveness of BSA as a potential carrier of 5-fluorouracil (5FU). 5-fluorouracil is a broad-spectrum anticancer drug targeting solid tumors. The research was carried out to estimate the physicochemical properties of the system using complementary measurement techniques. The optimization of the complex formation conditions made it possible to obtain significant correlations between the form of the drug and the effective localization of the active substance in the structure of the protein molecule. The presence of two amino groups in the 5FU structure contributes to the deprotonation of the molecule at high pH values (pH > 8) and the transition to the anionic form (AN1 and AN3). To investigate the binding affinity of the tautomeric form with BSA, UV-vis absorption, fluorescence quenching, zeta potential, QCM-D, and CD spectroscopic studies were performed. The experimental research was supported by molecular dynamics (MD) simulations and molecular docking. The simulations confirm the potential location of 5FU tautomers inside the BSA structure and on its surface.
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Affiliation(s)
- Olga Adamczyk
- Department of Physics, Cracow University of Technology, 30-084 Krakow, Poland (M.P.)
| | - Magdalena Szota
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, 31-355 Krakow, Poland (K.R.)
| | - Kamil Rakowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, 31-355 Krakow, Poland (K.R.)
| | - Magdalena Prochownik
- Department of Physics, Cracow University of Technology, 30-084 Krakow, Poland (M.P.)
| | - Daniel Doveiko
- Department of Physics, University of Strathclyde, Glasgow G4 0NG, UK; (D.D.); (Y.C.)
| | - Yu Chen
- Department of Physics, University of Strathclyde, Glasgow G4 0NG, UK; (D.D.); (Y.C.)
| | - Barbara Jachimska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, 31-355 Krakow, Poland (K.R.)
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Qais FA, Parveen N, Ahmad I, Husain FM, Khan A, Adil M. Multi-targeting of virulence factors of P. aeruginosa by β-lactam antibiotics to combat antimicrobial resistance. J Biomol Struct Dyn 2023:1-19. [PMID: 37904338 DOI: 10.1080/07391102.2023.2275181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023]
Abstract
Antimicrobial resistance poses a significant challenge to public health, especially in developing countries, due to a substantial rise in bacterial resistance. This situation has become so concerning that we are now at risk of losing the effectiveness of antibiotics altogether. Recent research has firmly established that bacteria engage in a process called quorum sensing (QS). QS regulates various functions, including nutrient scavenging, immune response suppression, increased virulence, biofilm formation and mobility. Pseudomonas aeruginosa, an opportunistic bacterial pathogen, plays a significant role in various medical conditions such as chronic wounds, corneal infections, burn wounds and cystic fibrosis. While antibiotics are effective in killing bacteria, only a few antibiotics, particularly those from the β-lactam group, have been studied for their impact on the quorum sensing of P. aeruginosa. Given the lack of concentrated efforts in this area, we have investigated the role of β-lactam antibiotics on various potential targets of P. aeruginosa. Based on their toxicological profiles and the average binding energy obtained through molecular docking, azlocillin and moxalactam have emerged as lead antibiotics. The binding energy for the docking of azlocillin and moxalactam with LasA was determined to be -8.2 and -8.6 kcal/mol, respectively. Molecular simulation analysis has confirmed the stable interaction of both these ligands with all three target proteins (LasI, LasA and PqsR) under physiological conditions. The results of this research underscore the effectiveness of azlocillin and moxalactam. These two antibiotics may be repurposed to target the quorum sensing of P. aeruginosa.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, UP, India
| | - Nagma Parveen
- Department of Zoology, Saifia College, Barkatullah University, Bhopal, India
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, UP, India
| | | | - Altaf Khan
- Department of Pharmacology, College of Pharmacy, King Saud University, Riyadh, KSA
| | - Mohd Adil
- Department of Environmental Sciences, Dalhousie University, Truro, NS, Canada
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Hedna R, DiMaio A, Robin M, Allegro D, Tatoni M, Peyrot V, Barbier P, Kovacic H, Breuzard G. 2-Aminothiazole-Flavonoid Hybrid Derivatives Binding to Tau Protein and Responsible for Antitumor Activity in Glioblastoma. Int J Mol Sci 2023; 24:15050. [PMID: 37894731 PMCID: PMC10606064 DOI: 10.3390/ijms242015050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Tau protein has been described for several decades as a promoter of tubulin assembly into microtubules. Dysregulation or alterations in Tau expression have been related to various brain cancers, including the highly aggressive and lethal brain tumor glioblastoma multiform (GBM). In this respect, Tau holds significant promise as a target for the development of novel therapies. Here, we examined the structure-activity relationship of a new series of seventeen 2-aminothiazole-fused to flavonoid hybrid compounds (TZF) on Tau binding, Tau fibrillation, and cellular effects on Tau-expressing cancer cells. By spectrofluorometric approach, we found that two compounds, 2 and 9, demonstrated high affinity for Tau and exhibited a strong propensity to inhibit Tau fibrillation. Then, the biological activity of these compounds was evaluated on several Tau-expressing cells derived from glioblastoma. The two lead compounds displayed a high anti-metabolic activity on cells related to an increased fission of the mitochondria network. Moreover, we showed that both compounds induced microtubule bundling within newly formed neurite-like protrusions, as well as with defection of cell migration. Taken together, our results provide a strong experimental basis to develop new potent molecules targeting Tau-expressing cancer cells, such as GBM.
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Affiliation(s)
- Rayane Hedna
- Faculté des Sciences Médicales et Paramédicales, Institut de Neurophysiopathologie (INP), UMR 7051, CNRS, Aix Marseille Université, 13005 Marseille, France; (R.H.); (D.A.); (M.T.); (V.P.); (P.B.); (H.K.)
| | - Attilio DiMaio
- Faculté de Pharmacie, Institut Méditerranéen de Biodiversité et Ecologie Marine et Continentale (IMBE), UMR 7263, CNRS, IRD 237, Aix-Marseille Université, 13005 Marseille, France; (A.D.); (M.R.)
| | - Maxime Robin
- Faculté de Pharmacie, Institut Méditerranéen de Biodiversité et Ecologie Marine et Continentale (IMBE), UMR 7263, CNRS, IRD 237, Aix-Marseille Université, 13005 Marseille, France; (A.D.); (M.R.)
| | - Diane Allegro
- Faculté des Sciences Médicales et Paramédicales, Institut de Neurophysiopathologie (INP), UMR 7051, CNRS, Aix Marseille Université, 13005 Marseille, France; (R.H.); (D.A.); (M.T.); (V.P.); (P.B.); (H.K.)
| | - Mario Tatoni
- Faculté des Sciences Médicales et Paramédicales, Institut de Neurophysiopathologie (INP), UMR 7051, CNRS, Aix Marseille Université, 13005 Marseille, France; (R.H.); (D.A.); (M.T.); (V.P.); (P.B.); (H.K.)
| | - Vincent Peyrot
- Faculté des Sciences Médicales et Paramédicales, Institut de Neurophysiopathologie (INP), UMR 7051, CNRS, Aix Marseille Université, 13005 Marseille, France; (R.H.); (D.A.); (M.T.); (V.P.); (P.B.); (H.K.)
| | - Pascale Barbier
- Faculté des Sciences Médicales et Paramédicales, Institut de Neurophysiopathologie (INP), UMR 7051, CNRS, Aix Marseille Université, 13005 Marseille, France; (R.H.); (D.A.); (M.T.); (V.P.); (P.B.); (H.K.)
| | - Hervé Kovacic
- Faculté des Sciences Médicales et Paramédicales, Institut de Neurophysiopathologie (INP), UMR 7051, CNRS, Aix Marseille Université, 13005 Marseille, France; (R.H.); (D.A.); (M.T.); (V.P.); (P.B.); (H.K.)
| | - Gilles Breuzard
- Faculté des Sciences Médicales et Paramédicales, Institut de Neurophysiopathologie (INP), UMR 7051, CNRS, Aix Marseille Université, 13005 Marseille, France; (R.H.); (D.A.); (M.T.); (V.P.); (P.B.); (H.K.)
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Manivel P, Marimuthu P, Ilanchelian M. Deciphering the binding site and mechanism of new methylene blue with serum albumins: A multispectroscopic and computational investigation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 300:122900. [PMID: 37244028 DOI: 10.1016/j.saa.2023.122900] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/28/2023] [Accepted: 05/17/2023] [Indexed: 05/29/2023]
Abstract
Herein, the interaction mechanism of new methylene blue (NMB) with human serum albumin (HSA) and bovine serum albumin (BSA) was carefully investigated both experimentally and conceptually, employing experimental and insilico analysis. The steady-state emission spectral studies showed that the emission intensity of HSA and BSA was quenched significantly by NMB. The findings of the Stern-Volmer and double logarithmic plot revealed that the observed emission quenching process was through a static quenching mechanism and the measured binding constant values (Kb) for HSA-NMB and BSA-NMB are 2.766 and 1.187 × 105 dm3 mol-1 respectively. The time-resolved fluorescence lifetime measurement and UV-vis absorption investigation further verify the complex formation between NMB and HSA/BSA. The assessment of thermodynamic parameters disclosed the binding process was spontaneous driven by hydrogen bonds (H-bond) and van der Waals interactions, which contributed a significant role in the complexation. Moreover, the secondary structural conformation and microenvironment of HSA/BSA were modified in the presence of NMB, as evidenced by circular dichroism and synchronous fluorescence data. Molecular docking study predicted a plausible binding mode of NMB inside the binding pocket of HSA and BSA. These results demonstrated that the stabilized NMB is found at the Subdomain IIA (site I) of both the proteins and the results were correlated well with the competitive binding assay. Additionally, the principal components analysis revealed less variation of docked poses for HSA, while, more dispersed docked poses were observed for the BSA model. This also highlights the effects of docking towards a modeled protein (BSA). Molecular dynamic (MD) simulation based binding free energy (ΔGmmgbsa) estimation obtained at 298, 303, 308 and 313 K, were in good agreement with our experimental (ΔGbind) values.
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Affiliation(s)
- Perumal Manivel
- Department of Chemistry, Bharathiar University, Coimbatore, Tamil Nadu, India; Bharathiar Cancer Theranostics Research Centre (RUSA-2.0), Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Parthiban Marimuthu
- Structural Bioinformatics Laboratory (SBL - Biochemistry) and Pharmaceutical Science Laboratory (PSL - Pharmacy), Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland
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Grabowska O, Samsonov SA, Chmurzyński L, Wyrzykowski D, Żamojć K. Investigation of hexacyanoferrate(II)/(III) charge-dependent interactions with bovine and human serum albumins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 293:122505. [PMID: 36809739 DOI: 10.1016/j.saa.2023.122505] [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: 09/21/2022] [Revised: 01/21/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
In the present paper, the binding interactions of highly negative-charged ions, namely hexacyanoferrates(II/III), i.e. [Fe(CN)6]4- and [Fe(CN)6]3- with bovine and human serum albumins (BSA and HSA, respectively) have been studied for the first time in an aqueous solution (10 mM cacodylate buffer of pH 7.0) using steady-state fluorescence spectroscopy, isothermal titration calorimetry, and CD spectroscopy supported by molecular dynamics-based computational approaches. The Stern-Volmer equation as well as its modifications suggested that hexacyanoferrates(II/III) effectively quenched the intrinsic fluorescence of the albumins through a static mechanism. The proteins under study possess only one binding site on the surface capable of binding one mole of hexacyanoferrates(II/III) ions per one mole of albumin (HSA or BSA). The formation of albumin complexes is an enthalpy-driven process (|ΔHITC| > |TΔSITC|). The strength of the interactions depends mainly on the type of albumin, and changes as follows: BSA-K3[Fe(CN)6] ∼ BSA-K4[Fe(CN)6] > HSA-K3[Fe(CN)6] ∼ HSA-K4[Fe(CN)6]. Finally, potential binding sites of bovine and human serum albumins have been investigated and discussed based on a competitive fluorescence displacement assay (with warfarin and ibuprofen as site markers) and molecular dynamics simulations.
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Affiliation(s)
- Ola Grabowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Lech Chmurzyński
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Dariusz Wyrzykowski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Krzysztof Żamojć
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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11
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Alomar SY. Studying the Mechanism of Interaction of Doxofylline with Human Lysozyme: A Biophysical and In Silico Approach. Molecules 2023; 28:molecules28083462. [PMID: 37110695 PMCID: PMC10146846 DOI: 10.3390/molecules28083462] [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: 12/29/2022] [Revised: 03/29/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023] Open
Abstract
In this study, multiple spectroscopic and computational methods were utilized to investigate the binding mechanism of doxofylline with lysozyme. The in vitro methods were used to obtain the binding kinetics and thermodynamics. UV-vis spectroscopy indicated the formation of complex between doxofylline and lysozyme. The Gibb's free energy and binding constant from UV-vis data was obtained as -7.20 kcal M-1 and 1.929 × 105 M-1, respectively. Doxofylline successfully quenched the fluorescence of lysozyme, confirming the formation of complex. The kq and Ksv values for the quenching of lysozyme's fluorescence by doxofylline were 5.74 × 1011 M-1 s-1 and 3.32 × 103 M-1, respectively. These values signified a moderate binding affinity between doxofylline and lysozyme. In synchronous spectroscopy, red shifts were observed for indicating the changes in microenvironment of lysozyme following the binding of doxofylline. The secondary structural analysis was determined using circular dichroism (CD) which revealed an increase in % α-helical as a result of doxofylline interaction. The binding affinity and flexibility of lysozyme upon complexation have been revealed via molecular docking and molecular dynamic (MD) simulations, respectively. According to the many parameters of the MD simulation, the lysozyme-doxofylline complex was stable under physiological conditions. All during the simulation time, hydrogen bonds were continuously present. The MM-PBSA binding energy for lysozyme and doxofylline binding was found to be -30.55 kcal mol-1.
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Affiliation(s)
- Suliman Yousef Alomar
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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12
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Madhav H, Abdel-Rahman SA, Hashmi MA, Rahman MA, Rehan M, Pal K, Nayeem SM, Gabr MT, Hoda N. Multicomponent Petasis reaction for the identification of pyrazine based multi-target directed anti-Alzheimer's agents: In-silico design, synthesis, and characterization. Eur J Med Chem 2023; 254:115354. [PMID: 37043996 DOI: 10.1016/j.ejmech.2023.115354] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/14/2023]
Abstract
Multi-target directed ligands (MTDLs) have recently attracted significant interest due to their exceptional effectiveness against multi-factorial Alzheimer's disease. The present work described the development of pyrazine-based MTDLs using multicomponent Petasis reaction for the dual inhibition of tau-aggregation and human acetylcholinesterase (hAChE). The molecular structure of synthesized ligands was validated by 1H & 13C NMR and mass spectrometry. The screened compounds were shown to have a strong inhibitory effect at 10 μM concentration against tau-oligomerization and hAChE, but only moderate inhibitory activity against Aβ42. Among all the compounds, the half-maximal inhibitory concentration (IC50) for 21 and 24 against hAChE were 0.71 μM and 1.09 μM, respectively, while they displayed half-maximal effective concentrations (EC50) values of 2.21 μM and 2.71 μM for cellular tau-oligomerization, respectively. Additionally, an MTT experiment using tau-expressing SH-SY5Y neuroblastoma cells revealed that 21 was more neuroprotective than the FDA-approved medication donepezil. Furthermore, an MD simulation study was performed to investigate the dynamics and stability of AChE-21 and AChE-24 complexes in an aqueous environment. The MM-PBSA calculations were performed to evaluate the binding of 21 and 24 with AChE, and the relative binding energy was calculated as -870.578 and -875.697 kJ mol-1, respectively. As a result, the study offered insight into the design of new MTDLs and highlighted 21 as a potential roadblock to the development of anti-AD medications.
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Affiliation(s)
- Hari Madhav
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Somaya A Abdel-Rahman
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY, 10065, USA; Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, Uttar Pradesh, India
| | - Md Ataur Rahman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Mohammad Rehan
- Max-Planck-Institute für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Kavita Pal
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Shahid M Nayeem
- Department of Chemistry, Aligarh Muslim University, Aligarh, 202002, Uttar Pradesh, India
| | - Moustafa T Gabr
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Nasimul Hoda
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India.
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13
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Revathi N, Sankarganesh M, Dhaveethu Raja J, Johnson Raja S, Gurusamy S, Nandini Asha R, Jeyakumar TC. Synthesis, spectral, DFT calculation, antimicrobial, antioxidant, DNA/BSA binding and molecular docking studies of bio-pharmacologically active pyrimidine appended Cu(II) and Zn(II) complexes. J Biomol Struct Dyn 2023; 41:14914-14928. [PMID: 37021479 DOI: 10.1080/07391102.2023.2196696] [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: 11/18/2022] [Accepted: 02/18/2023] [Indexed: 04/07/2023]
Abstract
A new pyrimidine derivative Schiff base (HL) [HL = 2-((4-amino-6-chloropyrimidin-2-ylimino)methyl)-4-nitrophenol] has been synthesized using 2,6-diamino-4-chloropyrimidine and 5-nitrosalicylaldehyde. Transition metal complexes of Cu(II) and Zn(II) complexes [CuL(OAc)] (1), [ZnL(OAc)] (2) are prepared with HL/metal(II) acetate with molar ratio of 1:1. The Schiff base (HL) and the complexes 1 and 2 are evaluated by UV-Visible, 1H-NMR, FT-IR, EI-MS and ESR spectral techniques. Complexes 1 and 2 are confirmed as square planar geometry. Electrochemical studies of the complexes 1 and 2 are used to analyse the quasi reversible process. Density Functional Theory (DFT) using the B3LYP/6-31++G(d,p) level basis set was used to get the optimised geometry and non-linear optical properties. The complexes 1 and 2 are good antimicrobial agents than Schiff base (HL). The interactions of the HL and complexes 1 and 2 with Calf Thymus (CT) DNA are investigated by electronic absorption methods and viscosity measurements. Various molecular spectroscopy techniques, such as UV absorption and fluorescence, were used to explore the mechanism of interaction between the BSA and the ligand HL and complexes 1 & 2 under physiological settings. Complexes 1 and 2 are act as potential antioxidants than free Schiff base (HL) by DPPH radical scavenging assay. Furthermore, the purpose of the molecular docking studies was to better understand how metal complexes interact with biomolecules (CT-DNA and BSA). From these biological analyses, complex 1 acts as good intercalator with CT DNA & BSA and potent antioxidant with DPPH radical than complex 2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nagaraj Revathi
- Department of Chemistry, Ramco Institute of Technology, Virudhunagar, Tamil Nadu, India
| | - Murugesan Sankarganesh
- Department of Chemistry, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
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14
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Qureshi MA, Amir M, Khan RH, Musarrat J, Javed S. Glycation reduces the binding dynamics of aflatoxin B 1 to human serum albumin: a comprehensive spectroscopic and computational investigation. J Biomol Struct Dyn 2023; 41:14797-14811. [PMID: 37021366 DOI: 10.1080/07391102.2023.2194000] [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: 01/04/2023] [Accepted: 02/25/2023] [Indexed: 04/07/2023]
Abstract
Aflatoxin B1 (AFB1), a potent mutagen, is synthesized by Aspergillus parasiticus and Aspergillus flavus. Human serum albumin (HSA) is a globular protein with diverse roles. As AFB1 is ingested with food and is transported in the body via blood, it becomes pertinent to comprehend the effect of the binding of this toxin on the structure and conformation of HSA, which may help to get insight into the toxic effect of the exposure of the mycotoxin. In this study, multi-spectroscopic approaches have been used to evaluate the binding efficiency of AFB1 with both the native HSA (nHSA) and the glycated HSA (gHSA). Steady-state fluorescence spectroscopy reveals the static type of fluorescence quenching in the fluorescence emission spectra of nHSA and gHSA in the presence of AFB1. The binding constant (Kb) is calculated to be 6.88 × 104 M-1 for nHSA, while a reduced Kb value of 2.95 × 104 M-1 has been obtained for gHSA. The circular dichroism study confirms the change in the secondary structure of nHSA and gHSA in the presence of AFB1, followed by alterations in the melting temperature (Tm) of nHSA and gHSA. In silico computational findings envisaged the amino acid residues and bonds involved in the binding of nHSA and gHSA with AFB1. The comprehensive study analyzes the binding effectiveness of AFB1 with nHSA and gHSA and shows reduced binding of AFB1 to gHSA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohd Aamir Qureshi
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Mohd Amir
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Javed Musarrat
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
| | - Saleem Javed
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
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15
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Ma J, Huang G, Mo C, Li J, Yan L, Zhang Q. Insights into the intercalative binding of benzo[b]fluoranthene with herring sperm DNA in vitro and its application. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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16
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Hashmi MA, Malik A, Arsalan A, Khan MA, Younus H. Elucidation of kinetic and structural properties of eye lens ζ-crystallin: an in vitro and in silico approach. J Biomol Struct Dyn 2023; 41:1178-1192. [PMID: 34927573 DOI: 10.1080/07391102.2021.2017351] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The Arabian Camelus dromedarius contains significant concentration of eye lens ζ-crystallin. This enzyme is also present in other life forms including humans, however in lower catalytic amounts. The recombinant camel ζ-crystallin was expressed in the E. coli BL21 (DE3) pLysS strain and purified using HisTrap column. The Km of the enzyme for 9,10-phenanthrenequinone (9,10-PQ) substrate and NADPH cofactor was determined to be 11.66 and 50.93 µM, respectively. The Vmax for 9,10-PQ and NADPH was obtained as 23.19 and 19.98 μM min-1, respectively. The optimum activity of the purified enzyme was found to be at pH 6.0 and at 55 °C. Different physico-chemical parameters were analysed including instability index (II), aliphatic index (AI) and the GRAVY index to establish proper characterization. The sequence of the recombinant ζ-crystallin was subjected to homology modelling using SWISS-MODEL webserver followed by validation of the modelled target structure. The evaluation of the modelled ζ-crystallin was performed by several parameters including Ramachandran plot, Z-score values followed by molecular dynamics (MD) simulation. The cumulative analysis of the physico-chemical, quantitative, qualitative and the essential dynamics of simulation of ζ-crystallin and its complexes with 9,10-PQ and NADPH helped in verifying the acceptable quality and stability of the ζ-crystallin structure.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Amiruddin Hashmi
- Enzymology Laboratory, Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Ajamaluddin Malik
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah Arsalan
- Enzymology Laboratory, Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Masood Alam Khan
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Hina Younus
- Enzymology Laboratory, Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
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17
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Laraoui H, Lanez E, Zegheb N, Adaika A, Lanez T, Benkhaled M. Anti‐Diabetic Activity of Flavonol Glucosides From
Fumana montana
Pomel: In vitro Analysis, In Silico Docking, ADMET Prediction, and Molecular Dynamics Simulations. ChemistrySelect 2023. [DOI: 10.1002/slct.202204512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- Habiba Laraoui
- Faculty of Matter Sciences Department of chemistry LCCE Laboratory University of Batna 5000 Batna Algeria
- Faculty of Exact and Natural Sciences Department of Matter Sciences University of Biskra BP 145 RP 07000 Biskra Algeria
| | - Elhafnaoui Lanez
- Department of Biochemistry University of El Oued 39000 El Oued Algeria
- Chemistry Department VTRS Laboratory University of El Oued B.P.789 39000 El Oued Algeria
| | - Nadjiba Zegheb
- Chemistry Department VTRS Laboratory University of El Oued B.P.789 39000 El Oued Algeria
| | - Aicha Adaika
- Chemistry Department VTRS Laboratory University of El Oued B.P.789 39000 El Oued Algeria
| | - Touhami Lanez
- Chemistry Department VTRS Laboratory University of El Oued B.P.789 39000 El Oued Algeria
| | - Mohammed Benkhaled
- Faculty of Matter Sciences Department of chemistry LCCE Laboratory University of Batna 5000 Batna Algeria
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18
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Hussain I, Fatima S, Ahmed S, Tabish M. Biophysical and molecular modelling analysis of the binding of β-resorcylic acid with bovine serum albumin. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2022.108175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Al-Jumaili MHA, Siddique F, Abul Qais F, Hashem HE, Chtita S, Rani A, Uzair M, Almzaien KA. Analysis and prediction pathways of natural products and their cytotoxicity against HeLa cell line protein using docking, molecular dynamics and ADMET. J Biomol Struct Dyn 2023; 41:765-777. [PMID: 34861809 DOI: 10.1080/07391102.2021.2011785] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Natural product such as flavonoids and their derivatives have a discernible capability to inhibit tumor formation and the growth of cancer cell, which have a vital link between diet and chronic disease prevention. Several plants and spices that contain flavonoid derivatives have been used in traditional medicine as disease preventative and therapeutic agents. Therefore, flavonoids could be used as chemotherapeutic drugs, indicating their potential clinical utility in cancer treatment. The purpose of this research was to discover and produce innovative pharmaceuticals from natural sources by introducing structural changes into flavonoids' backbones and changing their structures to improve biological activity and anticancer effects. In the current study, it was expected that the percent unbound values for the 15 compounds in human plasma would be low, ranging between 0.188 and 0.391. However, all compounds have a safe range and are not toxic to the brain. Compounds 2, 10, and 13 were shown to be permeable to the CNS (log PS > -3), but all other compounds had difficulty penetrating the CNS. Furthermore, all compounds had a low total clearance, ranging from 0.038 to 1.216 ml/min/kg, indicating that these compounds have a long half-life. None of the compounds caused skin sensitization (SS), and only compounds 1, 11, and 12 are expected to be AMES-positive, suggesting that the other compounds are not mutagenic. The result of the study showed based on the Drug-likeness and ADMET studies, only 3 compounds, including 3, 4, and 15, have a good pharmacokinetics propriety, the lowest toxicity, and good binding affinity towards Caspase 3 V266APDB (ID: 5I9B) as potential inhibitor candidates for the HeLa cell line, they have a low total clearance property and no AMES mutagenicity or hERG inhibition properties. These compounds (3,4,15) were examined to act as new cytotoxic drug candidates and would have an interest as starting point for designing compounds against the HeLa cell line.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Farhan Siddique
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.,Royal Institute of Medical Sciences (RIMS), Multan, Pakistan.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Pakistan Multan
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, UP, India
| | - Heba E Hashem
- Department of Chemistry, Faculty of Women, Ain Shams University, Cairo, Egypt
| | - Samir Chtita
- Department of Chemistry, Faculty of sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Abida Rani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Pakistan Multan
| | - Muhammad Uzair
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Pakistan Multan
| | - Kahtan A Almzaien
- Department of Medical Laboratory Techniques, Dijlah University College, Baghdad, Iraq
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20
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Akram M, Osama M, Hashmi MA, Kabir-Ud-Din. Molecular interaction of di-ester bonded cationic Gemini surfactants with pepsin: in vitro and in silico perspectives. J Biomol Struct Dyn 2023; 41:12276-12291. [PMID: 36695086 DOI: 10.1080/07391102.2023.2168759] [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: 10/01/2022] [Accepted: 01/01/2023] [Indexed: 01/26/2023]
Abstract
The implications of surfactant-enzyme/protein interactions in a variety of fields, including biotechnology, cosmetics, paints and pharmaceuticals, have attracted a lot of attention in contemporary studies. Herein, we have employed several in vitro and in silico techniques such as excitation and absorption spectroscopies, circular dichroism and FT-IR spectroscopies, density functional and molecular dynamics simulations to understand the interaction behavior of oxy-diester-based green cationic Gemini surfactants, N1,N1,N14,N14-tetramethyl-2,13-dioxo-N1,N14-dialkyl-3,6,12-tetraoxateradecane-1,14-diaminiumdichloride (abbreviated as Cm-E2O2-Cm, where 'm' stands for alkyl chain length, m = 12 and 14) with one of the main digestive proteins, pepsin. The spectroscopic techniques confirm the static quenching effect of surfactants on pepsin. The calculated physical parameters (Ksv, Kb and ΔG) and their order reveal the distinguished implications for the surfactants' chain lengths. The spontaneity of interaction was also confirmed by negative Gibbs free energy change values. The extrinsic spectroscopic study with pyrene as fluorescence probe, FT-IR and CD techniques indicated a potential conformational change in pepsin induced by the Gemini surfactants. DFT, docking and MD simulations provided the theoretical understanding regarding the quantum mechanical environment, location of binding and stability of the protein-surfactant complexation in energy terms. We believe this study will be a humble addition to our existing knowledge in the field of protein-surfactant interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohd Akram
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Mohammad Osama
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Kabir-Ud-Din
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
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21
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Butein Inhibits the Glycation of α-Crystallin: An Approach in Prevention of Retinopathy. J Fluoresc 2023:10.1007/s10895-023-03147-w. [PMID: 36648626 DOI: 10.1007/s10895-023-03147-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023]
Abstract
The aggregation of lens proteins induced by glycation is one of the key drivers of diabetic retinopathy and development of diabetic cataracts. Moreover, glycation also causes numerous alterations not only to the tertiary structure of lens proteins but also to serum proteins. There are also evidences of covalent crosslinking among lens crystallins resulting in development of cataract. In this article, the inhibitory potential of butein was tested against the glucose induced glycation and the aggregation α-crystallin (α-cry). The results showed that there was inhibition of advanced glycation products (78.28%) and early glycation products (86.30%) following the treatment of butein. Additionally, the presence of butein caused a significant improvement in the tested biochemical markers of glycation. The treatment with butein reduced the free lysine modification to 23.67%. The secondary and tertiary structural distortions of α-cry were also protected. The mechanism of inhibition further investigated at the molecular level using biophysical and computational techniques. The interaction data showed the butein exhibited strong affinity towards the α-cry. The binding event was entropically driven and energetically favourable. The Gibb's free energy of the interaction was found to be -5.99 to -7.17 kcal mol-1. The binding site of butein in α-cry was deciphered by molecular docking and the dynamics was studied using molecular dynamics (MD) simulations. The simulation data showed that butein formed stable complex with α-cry under physiological conditions. Most of the tested parameters from molecular simulations, such as secondary structure, was found to be stable. The data clearly show the potential of butein in inhibiting the glycation induced aggregation of α-cry and hence can be developed as useful inhibitor in the management of diabetic cataract and retinopathy.
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22
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Udnoor A, Lokolkar M, Yallur BC, Kale R, Kalasad MN, Katrahalli U, Manjunatha DH. Monitoring the interactions between bovine serum albumin and ZnO/Ag nanoparticles by spectroscopic techniques. J Biomol Struct Dyn 2023; 41:352-365. [PMID: 34821210 DOI: 10.1080/07391102.2021.2006788] [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: 01/03/2023]
Abstract
Inducing the bio-functionalization in noble metal nanoparticles like gold, silver, zinc is very important to accomplish their biocompatibility in biological activities. These metal nanoparticles are being rigorously used in bio-sensing tools keeping their remarkable properties in mind. Amongst the serum albumins, the most ample proteins in plasma are bovine serum albumin and human serum albumin. A broad variety of physiological functions of bovine serum albumin has made it a model protein for bio-functionalization. In the present study, ZnO/Ag nanoparticles were synthesized and characterized by SEM and XRD techniques and the interaction between bovine serum albumin and ZnO/Ag nanoparticles was evaluated by employing ultra-violet, steady state fluorescence, circular dichroism and FTIR spectroscopic techniques. Upon the excitation of bovine serum albumin, ZnO/Ag nanoparticles appreciably reduced the intrinsic fluorescence intensity of bovine serum albumin. The number of binding locations and apparent binding constants at different temperatures were calculated by the fluorescence quenching method. Static mechanism of quenching and conformational modifications in bovine serum albumin were also found.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhishek Udnoor
- PG Department of Chemistry, The Maratha Mandal Degree College, Belagavi, Karnataka, India
| | - Manjunath Lokolkar
- PG Department of Chemistry, The Maratha Mandal Degree College, Belagavi, Karnataka, India
| | - Basappa C Yallur
- Department of Chemistry, MS Ramaiah Institute of Technology, Bangalore, Karnataka, India
| | - Raju Kale
- PG Department of Chemistry, The Maratha Mandal Degree College, Belagavi, Karnataka, India
| | - Muttanagoud N Kalasad
- Department of Studies in Physics, Davangere University, Shivagangothri, Davangere, Karnataka, India
| | - Umesha Katrahalli
- PG Department of Chemistry, Vijaya College, Bangalore, Karnataka, India
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Qashqoosh MTA, Alahdal FAM, Manea YK, Zubair S, Khan RH, Khan AM, Naqvi S. Binding ability of roxatidine acetate and roxatidine acetate supported chitosan nanoparticles towards bovine serum albumin: characterization, spectroscopic and molecular docking studies. J Biomol Struct Dyn 2023; 41:106-124. [PMID: 34821213 DOI: 10.1080/07391102.2021.2004234] [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: 01/03/2023]
Abstract
The RxAc drug loaded on Tween80-chitosan-TPP nanoparticles (NRxAc) has been characterized and probed by UV-Vis, PXRD, FTIR, DLS and SEM technique. The physicochemical characteristics of NRxAc have been employed and evaluated for formulation of drug, particle size, external morphology, drug content and in vitro drug release. Multi-spectroscopic (i.e. fluorescence, UV-Vis, CD spectroscopy) and molecular docking techniques were also used to study the interaction of BSA with RxAc and NRxAc. RxAc and NRxAc quenched the fluorescence emission of BSA via a static quenching mechanism. The experimental data of Fluorescence demonstrated that the binding constant of RxAc and NRxAc were found around 104 L.mol-1, which suggests moderate binding affinity with BSA via hydrophobic forces. Through the site marker displacement experiments and molecular docking, the probable binding location of RxAc and NRxAc has been suggested in subdomain IB (site III) of BSA. Altogether, the results of present study can provide an important insight and a great deal of helpful information for future design of antiulcer drugs. Hence, The RxAc-loaded chitosan nanoparticles produced might be utilized as a successful tool for developing and using antiulcer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohsen T A Qashqoosh
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.,Department of Chemistry, University of Aden, Aden, Yemen
| | - Faiza A M Alahdal
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.,Department of Chemistry, Hodeidah University, Al Hudaydah, Yemen
| | - Yahiya Kadaf Manea
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.,Department of Chemistry, University of Aden, Aden, Yemen
| | - Swaleha Zubair
- Department of Computer science, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Amjad Mumtaz Khan
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Saeeda Naqvi
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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24
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Ouassaf M, Belaidi S, Chtita S, Lanez T, Abul Qais F, Md Amiruddin H. Combined molecular docking and dynamics simulations studies of natural compounds as potent inhibitors against SARS-CoV-2 main protease. J Biomol Struct Dyn 2022; 40:11264-11273. [PMID: 34315340 DOI: 10.1080/07391102.2021.1957712] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Main protease (Mpro) of SARS-CoV-2 is a key CoV enzyme that plays a pivotal role in mediating viral replication and transcription, making it an attractive drug target for SARS-CoV-2 the new strain of coronavirus. In this study, we evaluated biologically active compounds present in medicinal plants as potential SARS-CoV-2 Mpro inhibitors, using a molecular docking study with Autodock Vina software. Top seven compounds Afzelin, Phloroglucinol, Myricetin-3-O- rutinosid Tricin 7-neohesperidoside, Silybin, Kaempferol and Silychristin among 50 molecules of natural Origin (Algerian Medicinal plants) were selected which had better and significantly low binding energy as compared to the reference molecule with binding affinities of -9.3, -9.3, -9, -8.9, -8.5, 8.3 and -8.3 kcal mol-1 respectively. Then, we analyzed the ADME properties of the best 7 ligands using the Web server SwissADME. Two of small molecules have been shown to be the ideal candidates for further drug development. Finally, the stability of the both compounds complexed with Mpro was validated through molecular dynamics (MD) simulation, they displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations, moreover, Silybin could form more stable complex with Mpro than Silychristin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mebarka Ouassaf
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Salah Belaidi
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria.,Centre de Recherche en Sciences Pharmaceutiques (CRSP) la nouvelle ville Ali Mendjeli, Constantine, Algeria
| | - Samir Chtita
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Touhami Lanez
- VTRS Laboratory, Faculty of Sciences and Technology, University of El Oued, El Oued, Algeria
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Hashmi Md Amiruddin
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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25
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Insight into the Interaction Mechanism of HSA with Aztreonam: A Multispectroscopic and Computational Approach. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227858. [PMID: 36431957 PMCID: PMC9698515 DOI: 10.3390/molecules27227858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
Aztreonam is a Gram-negative bacteria-targeting synthetic monobactam antibiotic. Human serum albumin (HSA) plays an important role in the transference of pharmaceuticals, hormones, and fatty acids, along with other compounds, determining their biodistribution and physiological fate. Using several biophysical and in silico approaches, we studied the interaction of aztreonam with HSA under physiological environments in this study. Results confirm the formation of HSA-aztreonam complex where aztreonam showed moderate affinity towards HSA. A static mode of quenching was confirmed from the steady state fluorescence data. FRET findings also showed that there was a significant feasibility of energy transfer between HSA and aztreonam. Site marker displacement experimental conclusion suggested the binding site of aztreonam was the sub-domain IB of HSA. Circular dichroic spectroscopic analysis suggested that aztreonam interaction decreases the α-helical content of HSA. Changes in microenvironment were studied through synchronous fluorescence data. According to molecular docking results, the HSA-aztreonam complex is mostly maintained by non-covalent forces, with a binding energy of 7.7 kcal mol-1. The presence of a hydrogen bond, van der Waal interaction, and pi-anion interaction in the binding process, as well as conformational changes in HSA after binding with aztreonam, are all confirmed by molecular dynamic simulation.
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26
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Qais FA, Alomar SY, Imran MA, Hashmi MA. In-Silico Analysis of Phytocompounds of Olea europaea as Potential Anti-Cancer Agents to Target PKM2 Protein. Molecules 2022; 27:molecules27185793. [PMID: 36144527 PMCID: PMC9503632 DOI: 10.3390/molecules27185793] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/07/2022] [Accepted: 08/26/2022] [Indexed: 11/30/2022] Open
Abstract
Globally, cancer is the second leading cause of mortality and morbidity. The growth and development of cancer are extremely complex. It is caused by a variety of pathways and involves various types of enzymes. Pyruvate kinase M2 (PKM2) is an isoform of pyruvate kinase, that catalyses the last steps of glycolysis to produce energy. PKM2 is relatively more expressed in tumour cells where it tends to exist in a dimer form. Various medicinal plants are available that contain a variety of micronutrients to combat against different cancers. The phytocompounds of the olive tree (Olea europaea) leaves play an important role in inhibiting the proliferation of several cancers. In this study, the phytocompounds of olive leaf extract (OLE) were studied using various in silico tools, such as pkCSM software to predict ADMET properties and PASS Online software to predict anticancer activity. However, the molecular docking study provided the binding energies and inhibition constant and confirmed the interaction between PKM2 and the ligands. The dynamic behaviour, conformational changes, and stability between PKM2 and the top three hit compounds (Verbascoside (Ver), Rutin (Rut), and Luteolin_7_O_glucoside (Lut)) are studied by MD simulations.
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Affiliation(s)
- Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh UP-202002, India
- Correspondence: ; Tel.: +91-571-2703516
| | - Suliman Yousef Alomar
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Azhar Imran
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh UP-202002, India
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27
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Multi-spectroscopic, thermodynamic, and molecular docking/dynamic approaches for characterization of the binding interaction between calf thymus DNA and palbociclib. Sci Rep 2022; 12:14723. [PMID: 36042232 PMCID: PMC9427788 DOI: 10.1038/s41598-022-19015-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Studying the binding interaction between biological macromolecules and small molecules has formed the core of different research aspects. The interaction of palbociclib with calf thymus DNA at simulated physiological conditions (pH 7.4) was studied using different approaches, including spectrophotometry, spectrofluorimetry, FT-IR spectroscopy, viscosity measurements, ionic strength measurements, thermodynamic, molecular dynamic simulation, and docking studies. The obtained findings showed an apparent binding interaction between palbociclib and calf thymus DNA. Groove binding mode was confirmed from the findings of competitive binding studies with ethidium bromide or rhodamine B, UV–Vis spectrophotometry, and viscosity assessment. The binding constant (Kb) at 298 K calculated from the Benesi–Hildebrand equation was found to be 6.42 × 103 M−1. The enthalpy and entropy changes (∆H0 and ∆S0) were − 33.09 kJ mol−1 and 61.78 J mol−1 K−1, respectively, showing that hydrophobic and hydrogen bonds constitute the primary binding forces. As indicated by the molecular docking results, palbociclib fits into the AT-rich region of the B-DNA minor groove with four base pairs long binding site. The dynamic performance and stability of the formed complex were also evaluated using molecular dynamic simulation studies. The in vitro study of the intermolecular binding interaction of palbociclib with calf thymus DNA could guide future clinical and pharmacological studies for the rational drug scheming with enhanced or more selective activity and greater efficacy.
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28
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Arif A, Hashmi MA, Salam S, Younus H, Mahmood R. Interaction of the insecticide bioallethrin with human hemoglobin: biophysical, in silico and enzymatic studies. J Biomol Struct Dyn 2022:1-12. [PMID: 35950518 DOI: 10.1080/07391102.2022.2109756] [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: 10/15/2022]
Abstract
Bioallethrin is an insecticide that is widely used in households resulting in human exposure. Bioallethrin is cytotoxic to human erythrocytes. Here we have studied the interaction of bioallethrin with human hemoglobin (Hb) using in silico and biophysical approaches. Incubation of Hb (5 μM) with bioallethrin (1-50 µM) led to increase in absorbance at 280 nm while the Soret band at 406 nm was slightly reduced. The intrinsic fluorescence of Hb was enhanced with the appearance of a new peak around 305 nm. Synchronous fluorescence showed that the binding of bioallethrin to Hb mainly affects the tyrosine microenvironment. The structural changes in Hb were confirmed with a significant shift in CD spectra and about 25% loss of α-helix. Molecular docking and visualisation through Discovery studio confirmed the formation of Hb-bioallethrin complex with a binding energy of -7.3 kcal/mol. Molecular simulation showed the stability and energy dynamics of the binding reaction between bioallethrin and Hb. The structural changes induced by bioallethrin led to inhibition of the esterase activity of Hb. In conclusion, this study shows that bioallethrin forms a stable complex with human Hb which may lead to loss of Hb function in the body.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amin Arif
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Md Amiruddin Hashmi
- Department of Biotechnology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Samreen Salam
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Hina Younus
- Department of Biotechnology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Riaz Mahmood
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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29
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Zia Q, Rehman MT, Hashmi MA, Siddiqui S, Bin Dukhyil A, Ahmed MZ, Jamal A, Banawas S, Almalki SG, Owais M, Aldhafeeri HQ, Ibrahim IM, Alturaiki W, AlAjmi MF, Alsieni M, Alqurashi YE. Effect of Date Palm ( Phoenix dactylifera) Phytochemicals on Aβ 1-40 Amyloid Formation: An in-silico Analysis. Front Neurosci 2022; 16:915122. [PMID: 35958986 PMCID: PMC9359633 DOI: 10.3389/fnins.2022.915122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease and the most prevalent form of dementia. The generation of oxygen free radicals and oxidative damage is believed to be involved in the pathogenesis of AD. It has been suggested that date palm, a plant rich in phenolic compounds and flavonoids, can provide an alternative treatment to fight memory loss and cognitive dysfunction due to its potent antioxidant activity. Thus, we studied the effect of flavonoids present in date palm on Aβ1-40 amyloid formation using molecular docking and molecular dynamics simulation. AutoDock. Myricetin was used as a positive control drug. The flavonoids Diosmetin, Luteolin, and Rutin were found to be potent inhibitors of aggregation (docking energies ≤ -8.05 kcal mol-1) targeting Aβ1-40 fibrils (both 2LMO and 6TI5), simultaneously. Further screening by physicochemical properties and drug-likeness analysis suggested that all flavonoids except Rutin followed Lipinski's rule of five. Rutin was, thus, taken as a negative control (due to its violation of Lipinski's rule) to compare its dynamics with Diosmetin. Diosmetin exhibited the highest positive scores for drug likeness. Since Luteolin exhibited moderate drug-likeness and better absorption properties, it was also included in molecular dynamics simulation. Molecular dynamics of shortlisted compounds (Rutin, Diosmetin, and Luteolin) were performed for 200 ns, and the results were analyzed by monitoring root mean square deviations (RMSD), root mean square fluctuation (RMSF) analysis, the radius of gyration (Rg), and solvent accessible surface area (SASA). The results proved the formation of a stable protein-compound complex. Based on binding energies and non-bonded interactions, Rutin and Luteolin emerged as better lead molecules than Diosmetin. However, high MW (610.5), lowest absorption rate (16.04%), and more than one violation of Lipinski's rule make Rutin a less likely candidate as an anti-amyloidogenic agent. Moreover, among non-violators of Lipinski's rule, Diosmetin exhibited a greater absorption rate than Luteolin as well as the highest positive scores for drug-likeness. Thus, we can conclude that Diosmetin and Luteolin may serve as a scaffold for the design of better inhibitors with higher affinities toward the target proteins. However, these results warrant in-vitro and in-vivo validation before practical use.
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Affiliation(s)
- Qamar Zia
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Sahabjada Siddiqui
- Department of Biotechnology, Era's Lucknow Medical College and Hospital, Era University, Lucknow, India
| | - Abdulaziz Bin Dukhyil
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Mohammad Z. Ahmed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Azfar Jamal
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia
- Department of Biology, College of Science Al-Zulfi, Majmaah University, Majmaah, Saudi Arabia
| | - Saeed Banawas
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, United States
| | - Sami G. Almalki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Mohammad Owais
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Hamad Qasem Aldhafeeri
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Ibrahim M. Ibrahim
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Mohamed F. AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Alsieni
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yaser E. Alqurashi
- Department of Biology, College of Science Al-Zulfi, Majmaah University, Majmaah, Saudi Arabia
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Raza A, Mahmood R, Habib S, Talha M, Khan S, Hashmi MA, Mohammad T, Ali A. Fructosylation of human insulin causes AGEs formation, structural perturbations and morphological changes: an in silico and multispectroscopic study. J Biomol Struct Dyn 2022:1-13. [DOI: 10.1080/07391102.2022.2098820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Ali Raza
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Riaz Mahmood
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Safia Habib
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Mohd Talha
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Shifa Khan
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asif Ali
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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31
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Saeed A, Ejaz SA, Sarfraz M, Tamam N, Siddique F, Riaz N, Qais FA, Chtita S, Iqbal J. Discovery of Phenylcarbamoylazinane-1,2,4-Triazole Amides Derivatives as the Potential Inhibitors of Aldo-Keto Reductases (AKR1B1 & AKRB10): Potential Lead Molecules for Treatment of Colon Cancer. Molecules 2022; 27:molecules27133981. [PMID: 35807227 PMCID: PMC9268700 DOI: 10.3390/molecules27133981] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 12/12/2022] Open
Abstract
Both members of the aldo-keto reductases (AKRs) family, AKR1B1 and AKR1B10, are over-expressed in various type of cancer, making them potential targets for inflammation-mediated cancers such as colon, lung, breast, and prostate cancers. This is the first comprehensive study which focused on the identification of phenylcarbamoylazinane-1, 2,4-triazole amides (7a−o) as the inhibitors of aldo-keto reductases (AKR1B1, AKR1B10) via detailed computational analysis. Firstly, the stability and reactivity of compounds were determined by using the Guassian09 programme in which the density functional theory (DFT) calculations were performed by using the B3LYP/SVP level. Among all the derivatives, the 7d, 7e, 7f, 7h, 7j, 7k, and 7m were found chemically reactive. Then the binding interactions of the optimized compounds within the active pocket of the selected targets were carried out by using molecular docking software: AutoDock tools and Molecular operation environment (MOE) software, and during analysis, the Autodock (academic software) results were found to be reproducible, suggesting this software is best over the MOE (commercial software). The results were found in correlation with the DFT results, suggesting 7d as the best inhibitor of AKR1B1 with the energy value of −49.40 kJ/mol and 7f as the best inhibitor of AKR1B10 with the energy value of −52.84 kJ/mol. The other potent compounds also showed comparable binding energies. The best inhibitors of both targets were validated by the molecular dynamics simulation studies where the root mean square value of <2 along with the other physicochemical properties, hydrogen bond interactions, and binding energies were observed. Furthermore, the anticancer potential of the potent compounds was confirmed by cell viability (MTT) assay. The studied compounds fall into the category of drug-like properties and also supported by physicochemical and pharmacological ADMET properties. It can be suggested that the further synthesis of derivatives of 7d and 7f may lead to the potential drug-like molecules for the treatment of colon cancer associated with the aberrant expression of either AKR1B1 or AKR1B10 and other associated malignancies.
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Affiliation(s)
- Amna Saeed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Syeda Abida Ejaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
- Correspondence: (S.A.E.); (J.I.)
| | - Muhammad Sarfraz
- College of Pharmacy, Al Ain Campus, Al Ain University, Al Ain P.O. Box 64141, United Arab Emirates;
| | - Nissren Tamam
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, P.O Box 84428, Riyadh 11671, Saudi Arabia;
| | - Farhan Siddique
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-60174 Norrköping, Sweden;
- Department of Pharmacy, Royal Institute of Medical Sciences (RIMS), Multan 60000, Pakistan
| | - Naheed Riaz
- Department of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, UP, India;
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Sidi Othmane, Casablanca BP7955, Morocco;
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, Abbottabad Campus, COMSATS University Islamabad, Abbotabad 22060, Pakistan
- Correspondence: (S.A.E.); (J.I.)
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32
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Khamouli S, Belaidi S, Bakhouch M, Chtita S, Hashmi MA, Qais FA. QSAR modeling, molecular docking, ADMET prediction and molecular dynamics simulations of some 6-arylquinazolin-4-amine derivatives as DYRK1A inhibitors. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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33
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Khan MS, Althobaiti MS, Almutairi GS, Alokail MS, Altwaijry N, Alenad AM, Al-Bagmi MS, Alafaleq NO. Elucidating the binding and inhibitory potential of p-Coumaric acid against amyloid fibrillation and their cytotoxicity: Biophysical and docking analysis. Biophys Chem 2022; 291:106823. [DOI: 10.1016/j.bpc.2022.106823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/22/2022] [Accepted: 05/04/2022] [Indexed: 11/02/2022]
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34
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Chtita S, Fouedjou RT, Belaidi S, Djoumbissie LA, Ouassaf M, Qais FA, Bakhouch M, Efendi M, Tok TT, Bouachrine M, Lakhlifi T. In silico investigation of phytoconstituents from Cameroonian medicinal plants towards COVID-19 treatment. Struct Chem 2022; 33:1799-1813. [PMID: 35505923 PMCID: PMC9051495 DOI: 10.1007/s11224-022-01939-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 04/07/2022] [Indexed: 01/01/2023]
Abstract
In silico studies performed on the metabolites of four Cameroonian medicinal plants with a view to propose potential molecules to fight against COVID-19 were carried out. At first, molecular docking was performed for a set of 84 selected phytochemicals with SARS-CoV-2 main protease (PDB ID: 6lu7) protein. It was further followed by assessing the pharmacokinetics and pharmacological abilities of 15 compounds, which showed low binding energy values. As the screening criteria for their ADMET properties were performed, only two compounds have shown suitable pharmacological properties for human administration which were shortlisted. Furthermore, the stability of binding of these compounds was assessed by performing molecular dynamics (MD) simulations. Based on further analysis through molecular dynamics simulations and reactivity studies, it was concluded that only the Pycnanthuquinone C (17) and the Pycnanthuquinone A (18) extracted from the Pycnanthus angolensis could be considered as candidate inhibitors for targeted protein. Indeed, we expect that these compounds could show excellent in vitro and in vivo activity against SARS-CoV-2.
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35
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Khan RA, AlFawaz A, Farshori NN, Paul A, Jaafar MH, Alsalme A. Aminobenzimidazoles based (η
6
‐p‐cymene)Ruthenium (II) complexes as Nascent Anticancer Chemotherapeutics: Synthesis, Crystal Structure, DFT Studies, HSA Interactions, Molecular Docking, and Cytotoxicity. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Rais Ahmad Khan
- Department of Chemistry College of Science, King Saud University Riyadh KSA
| | - Amal AlFawaz
- Department of Chemistry College of Science, King Saud University Riyadh KSA
| | - Nida N. Farshori
- Department of Pharmacognosy College of Pharmacy, King Saud University Riyadh KSA
| | - Anup Paul
- Centro de Quimica Estrutural, Instituto Superior Tecnio, Unversidade de Lisboa Lisboa Portugal
| | - Mohammed H. Jaafar
- Department of Chemistry College of Science, King Saud University Riyadh KSA
| | - Ali Alsalme
- Department of Chemistry College of Science, King Saud University Riyadh KSA
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Ameliorative effect of pioglitazone on glucose induced glycation of α-crystallin: Management of complications associated with diabetic retinopathy. Int J Biol Macromol 2022; 209:107-116. [PMID: 35378163 DOI: 10.1016/j.ijbiomac.2022.03.202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/28/2022] [Accepted: 03/29/2022] [Indexed: 11/22/2022]
Abstract
The glycation and aggregation of lens proteins significantly contribute to the onset of diabetic cataracts as well as the retinopathy. The glycation exerts numerous alterations in the tertiary structural of proteins. Moreover, the covalent crosslinking of lens crystallins also contribute to the cataract formation. In this article, the effect of pioglitazone on glucose induced glycation and aggregation α-crystallin was examined. A remarkable inhibition of early glycation products (~80%) and advanced glycation products (~75%) was recorded by the treatment of pioglitazone. There was >75% recovery in biochemical marker (carbonyl content). The presence of 150 μM of pioglitazone reduced the free lysine modifications to 35%. Treatment of pioglitazone also protected the secondary structural alterations induced by glycation and inhibited the formation of protein aggregates. The interaction studies showed that pioglitazone interacted with α-crystallin via moderate binding affinity. The interaction between pioglitazone interacted and α-crystallin was energetically and entropically favourable. The complex of pioglitazone with studied protein stable in which RMSF, Rg, SASA, RMSD, and the secondary structural components was not affected. The findings show antiglycation activity of pioglitazone along with its mechanism of action highlighting the ability of drug to be possibly developed novel as glycation inhibitor.
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Design of novel benzimidazole derivatives as potential α-amylase inhibitors using QSAR, pharmacokinetics, molecular docking, and molecular dynamics simulation studies. J Mol Model 2022; 28:106. [DOI: 10.1007/s00894-022-05097-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/15/2022] [Indexed: 02/06/2023]
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Isolation, Identification, Spectral Studies and X-ray Crystal Structures of Two Compounds from Bixa orellana, DFT Calculations and DNA Binding Studies. CRYSTALS 2022. [DOI: 10.3390/cryst12030380] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
4,6-Diacetylresorcinol (1) and 3-O-methylellagic acid dihydrate (2), both biologically significant compounds, were extracted from Bixa orellana and studied using IR, 1H, and 13C NMR, and UV-vis spectroscopic techniques. X-ray crystallographic techniques were also used to establish the molecular structure of the isolated compounds 1 and 2. Geometric parameters, vibrational frequencies, and gauge including atomic orbital (GIAO) 1H and 13C NMR of 1 and 2 in the ground state were computed by the density functional theory (DFT) using B3LYP/6-311G(d,p) basis set backing up experimental studies and established the correct structure of isolated compounds. The parameters obtained from the combined DFT, and X-ray diffraction studies are mutually agreed to establish correct structures of 1 and 2. In addition, an electrostatic potential map and HOMO−LUMO energy gap were made using the DFT calculation to determine the distribution of energy and the chemical reactivity region of the isolated compounds. The current study also provides further insights into the interaction of compound 2 with ct-DNA using numerous biophysical and in silico techniques. Moreover, in silico studies indicate that compound 2 binds to the DNA in the minor groove. Lipinski’s rule of five revealed a higher tendency of compound 2 towards drug-likeness. The bioavailability and synthetic accessibility score for compound 2 was found to be 0.55 and 3.21, suggesting that compound 2 could serve as an effective therapeutic candidate.
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Yasmeen S, Qais FA, Rana M, Islam A, Rahisuddin. Binding and thermodynamic study of thalidomide with calf thymus DNA: Spectroscopic and computational approaches. Int J Biol Macromol 2022; 207:644-655. [PMID: 35278515 DOI: 10.1016/j.ijbiomac.2022.03.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 02/09/2023]
Abstract
The thalidomide-DNA interactions have been investigated in detail by numerous biophysical techniques such as UV-vis, dye displacement assay, viscosity, cyclic voltammetry, circular dichroism, molecular docking, molecular dynamic simulation, FT-IR and 1H NMR spectroscopy. CD spectroscopy, thermal denaturation and viscosity measurement explained that thalidomide is groove binder. Molecular docking analysis highlighted that thalidomide binds trough minor groove of calf thymus DNA which also confirmed from dye displacement experiment. To our knowledge, this is the first instance thalidomide was shown to binds with calf thymus DNA. Molecular dynamic simulation indicated that the thalidomide-DNA system was stabilized by electrostatic attraction as the main interaction and mode of binding is minor groove. Our study provides a better understanding to the DNA-thalidomide binding affinity and it mechanism. Overall, all these in formations can be used for further understanding the pharmacological effects of thalidomide.
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Affiliation(s)
- Shama Yasmeen
- Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Manish Rana
- Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Rahisuddin
- Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India.
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Parveen M, Aslam A, Siddiqui S, Tabish M, Alam M. Structure elucidation, DNA binding and molecular docking studies of natural compounds isolated from Crateva religiosa leaves. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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41
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Samreen, Qais FA, Ahmad I. In silico screening and in vitro validation of phytocompounds as multidrug efflux pump inhibitor against E. coli. J Biomol Struct Dyn 2022; 41:2189-2201. [PMID: 35067192 DOI: 10.1080/07391102.2022.2029564] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Multiple drug resistance (MDR) in bacteria has increased globally in recent times. This has reduced the efficacy of antibiotics and increasing the rate of therapeutic failure. Targeting efflux pump by natural and synthetic compounds is one of the strategies to develop an ideal broad-spectrum resistance-modifying agent. Very few inhibitors of AcrB from natural sources have been reported till date. In the current study, 19 phytocompounds were screened for efflux pump inhibitory activity against AcrB protein of E. coli TG1 using molecular docking studies. The molecular dynamics simulation provided stability the protein (AcrB) and its complex with chlorogenic acid under physiological conditions. Moreover, the detailed molecular insights of the binding were also explored. The Lipinski rule of 5 and the drug-likeness prediction was determined using Swiss ADME server, while toxicity prediction was done using admetSAR and PROTOX-II webservers. Chlorogenic acid showed the highest binding affinity (-9.1 kcal mol-1) with AcrB protein among all screened phytocompounds. Consequently, all the phytocompounds that accede to Lipinski's rule, demonstrated a high LD50 value indicating that they are non-toxic except the phytocompound reserpine. Chlorogenic acid and capsaicin are filtered out based on the synergy with tetracycline having FIC index of 0.25 and 0.28. The percentage increase of EtBr fluorescence by chlorogenic acid was 36.6% followed by piperine (24.2%). Chlorogenic acid may be a promising efflux pump inhibitor that might be employed in combination therapy with tetracycline against E. coli, based on the above relationship between in silico screening and in vitro positive efflux inhibitory activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Samreen
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
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Hussain I, Fatima S, Ahmed S, Tabish M. Deciphering the biomolecular interaction of β-resorcylic acid with human lysozyme: A biophysical and bioinformatics outlook. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Nour H, Abchir O, Belaidi S, Qais FA, Chtita S, Belaaouad S. 2D‐QSAR and molecular docking studies of carbamate derivatives to discover novel potent anti‐butyrylcholinesterase agents for Alzheimer's disease treatment. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hassan Nour
- Laboratory of Physical Chemistry of Materials Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca Casablanca Morocco
| | - Oussama Abchir
- Laboratory of Physical Chemistry of Materials Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca Casablanca Morocco
| | - Salah Belaidi
- Group of Computational and Medicinal Chemistry, LMCE Laboratory University of Biskra Biskra Algeria
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences Aligarh Muslim University Aligarh Uttar Pradesh India
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik Hassan II University of Casablanca Casablanca 7955 Morocco
| | - Said Belaaouad
- Laboratory of Physical Chemistry of Materials Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca Casablanca Morocco
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Hussain I, Fatima S, Siddiqui S, Ahmed S, Tabish M. Exploring the binding mechanism of β-resorcylic acid with calf thymus DNA: Insights from multi-spectroscopic, thermodynamic and bioinformatics approaches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119952. [PMID: 34052761 DOI: 10.1016/j.saa.2021.119952] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 06/12/2023]
Abstract
β-resorcylic acid (BR) is a phytochemical which is widely used in the food industry as a flavouring agent and preservative. It has also been found to exhibit antibacterial action against several types of food-borne bacteria. DNA is the main molecular target for many small molecules of therapeutic importance. Hence, the interest is rapidly growing among the researchers to elucidate the interaction between small molecules and DNA. Thus, paving the way to design novel DNA-specific drugs. In this study, an attempt was made to examine the mechanism of binding of BR with calf thymus DNA (ctDNA) with the help of various experiments based on spectroscopy and in silico studies. The spectroscopic studies like UV absorption and fluorescence affirmed the complex formation between BR and ctDNA. The observed binding constant was in the order of 103 M-1 which is indicative of the groove binding mechanism. These findings were further verified by dye-displacement assay, potassium iodide quenching, urea denaturation assay, the study of the effect of ssDNA, circular dichroism and DNA thermal denaturing studies. Different temperature-based fluorescence and isothermal titration calorimetry (ITC) experiments were employed to evaluate thermodynamic parameters. The analysis of thermodynamic parameters supports the enthalpically driven, exothermic and spontaneous nature of the reaction between BR and ctDNA. The forces involved in the binding process were mainly found to be hydrogen bonding, van der Waals and hydrophobic interactions. The results obtained from the molecular docking and molecular dynamics (MD) simulation were consistent with the in vitro experiments, which support the groove binding mode of BR with ctDNA.
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Affiliation(s)
- Irfan Hussain
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India
| | - Sana Fatima
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India
| | - Sharmin Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India
| | - Shahbaz Ahmed
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India.
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In silico and multi-spectroscopic analyses on the interaction of 5-amino-8-hydroxyquinoline and bovine serum albumin as a potential anticancer agent. Sci Rep 2021; 11:20187. [PMID: 34642420 PMCID: PMC8511024 DOI: 10.1038/s41598-021-99690-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/28/2021] [Indexed: 12/20/2022] Open
Abstract
5-Amino-8-hydroxyquinoline (5A8HQ), an amino derivative of 8-hydroxyquinoline, has become a potential anticancer candidate because of its promising proteasome inhibitory activity to overcome and yet synergize bortezomib for fighting cancers. Therefore, in this study, its physicochemical properties and interaction activities with serum protein have extensively been elucidated by both in vitro and in silico approaches to fulfill the pharmacokinetic and pharmacodynamic gaps. 5A8HQ exhibited the drug-likeness properties, where oral administration seems to be a route of choice owing to its high-water solubility and intestinal absorptivity. Multi-spectroscopic investigations suggested that 5A8HQ tended to associate with bovine serum albumin (BSA), a representative of serum protein, via the ground-state complexation. It apparently bound in a protein cleft between subdomains IIA and IIIA of BSA as suggested by the molecular docking and molecular dynamics simulations. The binding was mainly driven by hydrogen bonding and electrostatic interactions with a moderate binding constant at 104 M−1, conforming with the predicted free fraction in serum at 0.484. Therefore, 5A8HQ seems to display a good bioavailability in plasma to reach target sites and exerts its potent pharmacological activity. Likewise, serum albumin is a good candidate to be reservoir and transporter of 5A8HQ in the circulatory system.
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Zahin M, Bokhari NA, Ahmad I, Husain FM, Althubiani AS, Alruways MW, Perveen K, Shalawi M. Antioxidant, antibacterial, and antimutagenic activity of Piper nigrum seeds extracts. Saudi J Biol Sci 2021; 28:5094-5105. [PMID: 34466087 PMCID: PMC8381071 DOI: 10.1016/j.sjbs.2021.05.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/20/2022] Open
Abstract
Piper nigrum is a widely used plant in traditional remedies and known for its numerous biological properties. However, fraction-based antioxidant activity and their antimutagenic potential are not yet fully investigated. Different extracts of the seeds P. nigrum were obtained by sequential extraction in different solvents. All extracts were evaluated for antibacterial and antioxidant activities using different methods. The most active fraction was analyzed for antimutagenic activity using the Ames Salmonella test. The antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) was found to be more prominent compared to ESβL producing Klebsiella pneumoniae isolates. The MIC values were found to be lower against MRSA than K. pneumoniae. The extract showing highest antioxidant activity (methanol extract) was further tested for antimutagenic activity both against direct and indirect-acting mutagens. A varying level of antimutagenic activity was shown by methanol extract at highest tested concentration (200 µg/plate). Alkaloids, phenols, and flavonoids were detected as major class of compounds in methanol extract. Gas chromatography-mass spectrometry (GC–MS) analysis showed the presence of various phytocompounds. Based on molecular docking of two major active phytocompounds (piperine and copaene), they were found to interact at the minor groove of DNA. Molecular dynamics (MD) simulation revealed that both the ligands were quite stable with DNA under physiological conditions. The ability of phytocompounds to interact with DNA might be reducing the interaction of mutagens and could be one of the possible mechanism of anti-mutagenic activity of P. nigrum extract. This study highlights the antioxidant and antimutagenic potential of Piper nigrum. The role of phytocompounds present in the bioactive extract is needed to be explored further for herbal drug research.
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Affiliation(s)
- Maryam Zahin
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh-202002, UP, India
| | - Najat A. Bokhari
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Corresponding author.
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh-202002, UP, India
- Corresponding author.
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Mashael W. Alruways
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Shaqra, Saudi Arabia
| | - Kahkashan Perveen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Misfera Shalawi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Qais FA, Khan MS, Ahmad I, Husain FM, Al-Kheraif AA, Arshad M, Alam P. Plumbagin inhibits quorum sensing-regulated virulence and biofilms of Gram-negative bacteria: in vitro and in silico investigations. BIOFOULING 2021; 37:724-739. [PMID: 34396840 DOI: 10.1080/08927014.2021.1955250] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
The global rise in antimicrobial resistance and lack of discovery of new antimicrobials have created serious concerns. Targeting quorum sensing (QS) and biofilms of pathogenic bacteria is considered a promising approach in antimicrobial drug discovery. This study explored the inhibitory effect of plumbagin against biofilms and QS of Chromobacterium violaceum, Serratia marcescens and Pseudomonas aeruginosa. Violacein production in C. violaceum 12472 was reduced by >80%. The virulent traits of P. aeruginosa PAO1 such as pyocyanin, rhamnolipid and proteases were also inhibited at sub-minimum inhibitory concentrations. Moreover, the biofilms of the test bacteria were reduced by 56-70%. Plumbagin reduced the bacterial adherence and colonization on solid surface. Computational studies gave closer insights regarding the possible modes of action. Molecular dynamics simulations revealed that the protein complexes were quite stable under physiological conditions. This study provides both experimental and computational evidence regarding the efficacy of plumbagin against biofilms and the QS-controlled virulence factors of Gram-negative bacteria.
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Affiliation(s)
- Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Mohammad Shavez Khan
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, King Saud University, Riyadh, Saudi Arabia
| | - Abdulaziz Abdullah Al-Kheraif
- Dental Biomaterials Research Chair, Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Arshad
- Dental Biomaterials Research Chair, Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Al-kharj, Kingdom of Saudi Arabia
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Qais F, Khan MS, Ahmad I, Husain FM, Khan RA, Hassan I, Shahzad SA, AlHarbi W. Coumarin Exhibits Broad-Spectrum Antibiofilm and Antiquorum Sensing Activity against Gram-Negative Bacteria: In Vitro and In Silico Investigation. ACS OMEGA 2021; 6:18823-18835. [PMID: 34337222 PMCID: PMC8320077 DOI: 10.1021/acsomega.1c02046] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/07/2021] [Indexed: 05/07/2023]
Abstract
Quorum sensing (QS) and biofilm inhibition are recognized as the novel drug targets for the broad-spectrum anti-infective strategy to combat the infections caused by drug-resistant bacterial pathogens. Many compounds from medicinal plants have been found to demonstrate anti-infective activity. However, broad-spectrum anti-QS and antibiofilm efficacy and their mode of action are poorly studied. In this study, the efficacy of coumarin was tested against QS-regulated virulent traits of Gram-negative bacteria. Coumarin inhibited the production of violacein pigment in Chromobacterium violaceum 12472 by 64.21%. Similarly, there was 87.25, 70.05, 76.07, 58.64, 48.94, and 81.20% inhibition of pyocyanin, pyoverdin, and proteolytic activity, lasB elastase activity, swimming motility, and rhamnolipid production, respectively, in Pseudomonas aeruginosa PAO1. All tested virulence factors of Serratia marcescens MTCC 97 were also suppressed by more than 50% at the highest sub-minimum inhibitory concentration. Moreover, the biofilms of bacterial pathogens were also inhibited in a dose-dependent manner. Molecular docking and molecular dynamics (MD) simulation gave insights into the possible mode of action. The binding energy obtained by docking studies ranged from -5.7 to -8.1 kcal mol-1. Coumarin was found to be docked in the active site of acylhomoserine lactone (AHL) synthases and regulatory proteins of QS. MD simulations further supported the in vitro studies where coumarin formed a stable complex with the tested proteins. The secondary structure of all proteins showed a negligible change in the presence of coumarin. Computational studies showed that the possible mechanisms of anti-QS activity were the inhibition of AHL synthesis, antagonization of QS-regulatory proteins, and blocking of the receptor proteins. The findings of this study clearly highlight the potency of coumarin against the virulence factors of Gram-negative bacterial pathogens that may be developed as an effective inhibitor of QS and biofilms.
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Affiliation(s)
- Faizan
Abul Qais
- Department
of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Mohammad Shavez Khan
- Department
of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Iqbal Ahmad
- Department
of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
- . Phone: +91-571-2703516, +91-9897902936. Fax: +91-571-2703516
| | - Fohad Mabood Husain
- Department
of Food Science and Nutrition, King Saud
University, Riyadh 11451, Saudi Arabia
| | - Rais Ahmad Khan
- Department
of Chemistry, King Saud University, Riyadh 11451, Saudi Arabia
| | - Iftekhar Hassan
- Department
of Zoology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Syed Ali Shahzad
- Department
of Food Science and Nutrition, King Saud
University, Riyadh 11451, Saudi Arabia
| | - Walaa AlHarbi
- Department
of Chemistry, Faculty of Science, King Khalid
University, P.O. Box 9004, Abha 62529, Saudi Arabia
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Rath B, Abul Qais F, Patro R, Mohapatra S, Sharma T. Design, synthesis and molecular modeling studies of novel mesalamine linked coumarin for treatment of inflammatory bowel disease. Bioorg Med Chem Lett 2021; 41:128029. [PMID: 33839254 DOI: 10.1016/j.bmcl.2021.128029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel diseases (IBD) are continuous idiopathic inflammation of GIT. Ulcerative colitis, inflammation of the colonic or rectal mucosa has no known medical cure and its treatment is aimed at reducing the signs and symptoms associated with the disorders, induction and maintenance of remission. In this study, we have reported the synthesis of mesalamine and coumarin linked together by a diazo group. The compound was characterized by various spectroscopic methods. Therapeutic potential of the synthesized compound was investigated through acetic acid induced ulcerative rat model. Pharmacokinetic properties were predicted for the compounds by ADMET related descriptors. Molecular docking studies were conducted with four proteins (COX-2, MMP-9, TNF-α and MPO) to examine the interaction of mesalamine (MS) and mesalamine coumarin derivative (MS-CU). Moreover, molecular dynamic simulations were carried out to study the dynamics and stability of the complexes in solvent system. The binding energy of MS-CU with MPO, COX-2, MMP-9 and TNF-α was found to be -9.5, -10.4, -9.2 and -8.4 kcal/mol respectively. MS-CU exhibited higher binding affinity towards all tested proteins than MS. Molecular dynamic simulation reveals that both MS and MS-CU formed a stable complex with all test proteins in aqueous system. Overall binding energy of MS-CU was more than MS showing stronger affinity towards the test portions. In conclusion, Mesalamine-coumarin derivative reduces colonic damage in acetic acid induced ulcerative colitis in rat model, and therefore may prove to be effective in the management of IBD.
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Affiliation(s)
- Biswabhusan Rath
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Siksha 'O'Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Randeep Patro
- Department of Pharmacology, School of Pharmaceutical Sciences, Siksha 'O'Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Sujata Mohapatra
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Siksha 'O'Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India.
| | - Tripti Sharma
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Siksha 'O'Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India.
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