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Farhat N, Khanam T, Noor S, Khan AU. Structural insight into the binding mode of cefotaxime and meropenem to TEM-1, SHV-1, KPC-2, and Amp-C type beta-lactamases. Cell Biochem Biophys 2024:10.1007/s12013-024-01284-y. [PMID: 38730202 DOI: 10.1007/s12013-024-01284-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
Antimicrobial resistance is an emerging threat to public health around the world. The study employs computational and biophysical methods to investigate the properties of cefotaxime and meropenem's binding to various beta-lactamases like TEM-1, SHV-1, KPC-2, and Amp-C. The enzyme kinetics of purified proteins revealed an increase in Michaelis constant (Km) value in the presence of meropenem and cefotaxime, indicating a decrease in enzyme affinity for nitrocefin. Proteins interact with meropenem/cefotaxime, causing quenching through complex formation. All proteins have one binding site, and binding constant (Kb) values are 104, indicating strong interaction. The study found that meropenem and cefotaxime had high fitness scores for Amp-C, KPC-2,TEM-1 and SHV-1, with binding energy ranging from -7.4 to -7.8, and hydrogen bonds between them. Molecular Dynamic simulation of protein-ligand complexes revealed cefotaxime-binding proteins have slightly lower Root Mean Square Deviation(RMSD) than meropenem-binding proteins, indicating stable association antibiotics with these proteins.
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Affiliation(s)
- Nabeela Farhat
- Antimicrobial Resistance Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Tasneem Khanam
- Antimicrobial Resistance Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Saba Noor
- Antimicrobial Resistance Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Asad U Khan
- Antimicrobial Resistance Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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Rogalewicz B, Pitucha M, Świątkowski M, Humeniuk E, Adamczuk G, Drózd M, Karczmarzyk Z, Kuśmierek E, Strzelec K, Raducka A, Wysocki W, Olender A, Kozub A, Kowalczuk D, Poleszak E, Czylkowska A. Structure-activity relationship and cytotoxicity of the new thiosemicarbazide derivatives and their Cu(II) complexes against prostate and melanoma cancer cells. Arch Biochem Biophys 2024; 755:109955. [PMID: 38460659 DOI: 10.1016/j.abb.2024.109955] [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: 12/22/2023] [Revised: 02/15/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
In this study, eighteen new ligands (B1-B18) containing a thiosemicarbazide core were synthesized and characterized in terms of physicochemical properties, molecular docking and in vitro biological activity. The structures of eleven ligands were investigated using X-Ray diffraction and Hirschfeld Surface analysis. To study the structure-activity relationship, the organic ligands contained pyridin-2-ylmethyl, pyridin-3-ylmethyl or pyridin-4-ylmethyl moieties and various substituents. Their pharmakokinetic profiles and molecular docking results suggest high potential as new drug candidates. The complexing ability of the selected organic ligands was also evaluated, yielding five new Cu(II) complexes (Cu(B1)Cl2, Cu(B4)Cl2, Cu(B10)Cl2, Cu(B17)Cl2, Cu(B18)Cl2). The obtained results suggest the formation of the polymeric structures. All organic ligands and Cu(II) complexes were tested for anticancer activity against prostate and melanoma cancer cells (PC-3, DU-145, LNCaP, A375, G-361, SK-MEL-28) and normal fibroblasts (BJ), as well as antimicrobial activity against six selected bateria strains. Among B1-B18 compounds, B3, B5, B9, B10, B12 and B14 exhibited cytotoxic activity. The studied Cu(II) complexes were in general more active, with Cu(B1)Cl2 exhibiting antincancer activity agains all three prostate cancer cells and Cu(B10)Cl2 reaching the IC50 value equal to 88 μM against G-361 melanoma cells. Several compounds also exhibited antimicrobial activity against gram-positive and gram-negative bacteria. It was found that the type of specific substituents, especially the presence of -chloro and -dichloro substituents had a greated impact on the cytotoxicity than the position of the nitrogen atom in the pyridylacetyl moiety.
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Affiliation(s)
- Bartłomiej Rogalewicz
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924, Lodz, Poland.
| | - Monika Pitucha
- Independent Radiopharmacy Unit, Faculty of Pharmacy, Medical University of Lublin, Chodzki 4a, 20-093, Lublin, Poland
| | - Marcin Świątkowski
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924, Lodz, Poland
| | - Ewelina Humeniuk
- Independent Medical Biology Unit, Faculty of Pharmacy, Medical University of Lublin, Jaczewskiego 8b, 20-093, Lublin, Poland
| | - Grzegorz Adamczuk
- Independent Medical Biology Unit, Faculty of Pharmacy, Medical University of Lublin, Jaczewskiego 8b, 20-093, Lublin, Poland
| | - Monika Drózd
- Independent Radiopharmacy Unit, Faculty of Pharmacy, Medical University of Lublin, Chodzki 4a, 20-093, Lublin, Poland
| | - Zbigniew Karczmarzyk
- Department of Chemistry, University of Siedlce, 3 Maja 54, 08-110, Siedlce, Poland
| | - Elżbieta Kuśmierek
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924, Lodz, Poland
| | - Krzysztof Strzelec
- Institute of Polymer & Dye Technology, Faculty of Chemistry, Lodz University of Technology, Stefanowskiego 12/16, 90-924, Lodz, Poland
| | - Anita Raducka
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924, Lodz, Poland
| | - Waldemar Wysocki
- Department of Chemistry, University of Siedlce, 3 Maja 54, 08-110, Siedlce, Poland
| | - Alina Olender
- Chair and Department of Medical Microbiology, Medical University of Lublin, Chodzki 1, 20-093, Lublin, Poland
| | - Anna Kozub
- Department of Bioanalytics, Faculty of Biomedicine, Medical University of Lublin, Jaczewskiego 8b, 20-090, Lublin, Poland
| | - Dorota Kowalczuk
- Chair and Department of Medicinal Chemistry, Faculty of Pharmacy, Medical University of Lublin, Jaczewskiego 4, 20-090, Lublin, Poland
| | - Ewa Poleszak
- Laboratory of Preclinical Testing, Chair and Department of Applied and Social Pharmacy, Medical University of Lublin, Chodzki 1, 20-093, Lublin, Poland
| | - Agnieszka Czylkowska
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924, Lodz, Poland.
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3
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Li X, Sun X. 1,3-Proton Transfer of Pyridoxal 5'-Phosphate Schiff Base in the Branched-Chain Aminotransferase: Concerted or Stepwise Mechanism? J Phys Chem B 2024; 128:77-85. [PMID: 38131279 DOI: 10.1021/acs.jpcb.3c05875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The branched-chain aminotransferase from Mycobacterium tuberculosis (MtIlvE) is a pyridoxal 5'-phosphate (PLP) dependent enzyme, and it is essential for the synthesis of the branched-chain amino acids. Ketimine is an important intermediate in the catalytic process. We have investigated the mechanism of ketimine formation and the energy landscape using the multiple computational methods. It is found that the 1,3-proton transfer involved in ketimine formation occurs through a stepwise process rather than a one-step process. Lys204 is identified as a key residue for ligand binding and as a base that abstracts the Cα proton from the PLP-Glu Schiff base, yielding a carbanionic intermediate. The first proton transfer is the rate-limiting step with an energy barrier of 17.8 kcal mol-1. Our study disclosed the detailed pathway of the proton transfer from external aldimine to ketimine, providing novel insights into the catalytic mechanism of other PLP-dependent enzymes.
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Affiliation(s)
- Xue Li
- School of Life Sciences, Changchun Normal University, Changchun 130023, People's Republic of China
| | - Xiaoli Sun
- Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
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Liang J, Li H, Ren M, Zhou M, Han J, Zhou W, Kong F, Fakayode OA, Ur Rehman A, Fapohunda FO, Zhou C. Lignin-ultrasound method: Enhancement of antimicrobial capacity of MoS 2-containing films. Int J Biol Macromol 2023; 252:126509. [PMID: 37633551 DOI: 10.1016/j.ijbiomac.2023.126509] [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: 05/23/2023] [Revised: 07/27/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
To improve the antimicrobial ability of MoS2-containing films, we used lignin and triple-frequency ultrasound for liquid-phase exfoliation (LPE) to obtain MoS2 nanosheets. Photoresponsive antimicrobial films with MoS2 nanosheets, lignin, polyvinyl alcohol and deep eutectic solvents were subsequently prepared. Lignin functionalized the MoS2 nanosheets by chemically linking with S in MoS2 and significantly improved the exfoliation efficiency. Tri-frequency ultrasound produces beneficial effects on the LPE process by creating a more homogeneous sound field and a stronger degree of cavitation. The concentration of MoS2 nanosheets in the exfoliating solution could reach 1.713 mg/mL under the effect of lignin-ultrasound. The antimicrobial ability of the films was analyzed, and the colony-forming units of E. coli and S. aureus could be reduced from 7 × 106 to 1 × 106 cfu/mL under the irradiation of infrared. The lignin in the film undergoes depolymerization and demethoxylation under the irradiation of infrared to have a more phenolic hydroxyl structure, which confers the growth inhibition ability of the films for bacteria that cannot be in close contact with the film. The method we used has some significance for the preparation of MoS2 nanosheets, and composite films prepared from MoS2, and lignin can be used in food packaging, wound antimicrobials, and other fields.
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Affiliation(s)
- Jiakang Liang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Haoxin Li
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Manni Ren
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Man Zhou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jingyi Han
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Wenhao Zhou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Fangong Kong
- State Key Laboratory of Biobased Material and Green Papermaking, Key Laboratory of Pulp and Paper Science & Technology of Ministry of Education/Shandong Province, Faculty of Light Industry, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Olugbenga Abiola Fakayode
- Department of Mechanical Engineering, 10-263 Donadeo Innovation Centre for Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Abd Ur Rehman
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | | | - Cunshan Zhou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
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Rathi R. Potential inhibitors of FemC to combat Staphylococcus aureus: virtual screening, molecular docking, dynamics simulation, and MM-PBSA analysis. J Biomol Struct Dyn 2023; 41:10495-10506. [PMID: 36524526 DOI: 10.1080/07391102.2022.2157328] [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: 09/15/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
FemC is a methicillin resistance factor involved in the alterations of peptidoglycan and glutamine synthesis in Staphylococcus aureus. To identify the potent antibacterial agents, antibacterial molecules were screened against the predicted and validated FemC model. Based on docking scores, presence of essential interactions with active site residues of FemC, pharmacokinetic, and ADMET properties, six candidates were shortlisted and subjected to molecular dynamics to evaluate the stability of FemC-ligand complexes. Further, per residue decomposition analysis and Molecular Mechanics/Poisson-Boltzmann Surface Area (MMPBSA) analysis confirmed that S15, M16, S17, R31, R43, Q47, K48 and R49 of FemC played a vital role in the formation of lower energy stable FemC-inhibitor(s) complexes. Therefore, in the present study, the reported six molecules (Z317461228, Z92241701, Z30923155, Z30202349, Z2609517102 and Z92470167) may pave the path to design the scaffold of novel potent antimicrobials against S. aureus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Rathi
- Amity School of Applied Sciences, Amity University Haryana, Gurgaon, Haryana, India
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6
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Kaur A, Mandal D. Computational identification and exploration of novel FGFR tyrosine kinase inhibitors for the treatment of cholangiocarcinoma. J Biomol Struct Dyn 2023:1-12. [PMID: 37897189 DOI: 10.1080/07391102.2023.2274975] [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: 06/12/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023]
Abstract
Tyrosine kinase inhibitors are a specific drug class revolutionizing cancer treatment. FGFR (Fibroblast Growth Factor Receptor) is a member of the receptor tyrosine kinase family that has been involved in various alterations which have been increasingly recognized as critical molecular drivers in cholangiocarcinoma, a malignant tumor originating from bile duct epithelial cells. The paper focuses on stepwise computational investigations for the discovery of novel inhibitors of FGFR using pharmacophore modeling, virtual screening, docking, ADMET analysis, molecular dynamics, and knowledge-based structure-activity relationship. To begin with, we have considered a library of 120314868 compounds from the ZINC 15 database through pharmacophore modeling, which was narrowed down to 110 having binding affinity >-8.0 kcal mol-1. The 110 compounds were analyzed using virtual screening and compared with the FDA-approved drug pemigatinib, which provided the 34 hits with binding affinities >-6.5 kcal mol-1. Finally, the top 4 hits were considered for docking, and ADMET property analysis for drug-likeness. MD and MM-GBSA analysis were performed to predict the binding free energy of these chemicals and determine their stability. To gain insight into the structure and binding interactions of these compounds, knowledge-based SAR analyses were performed using their electrostatic potential maps computed with DFT. Several techniques were employed to build improved inhibitors based on these SAR, and they were then analyzed utilizing ADMET, MD studies, and MM-GBSA analyses. Finally, the results suggested that the identified four compounds and developed inhibitors from this current work can be employed effectively as prospective FGFR inhibitors for treating Cholangiocarcinoma.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amanpreet Kaur
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, India
| | - Debasish Mandal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, India
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Xie P, Gao Y, Wu C, Li X, Yang Y. The inhibitory mechanism of echinacoside against Staphylococcus aureus Ser/Thr phosphatase Stp1 by virtual screening and molecular modeling. J Mol Model 2023; 29:320. [PMID: 37725157 DOI: 10.1007/s00894-023-05723-0] [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: 06/26/2023] [Accepted: 09/09/2023] [Indexed: 09/21/2023]
Abstract
CONTEXT Stp1 is a new potential target closely related to the pathogenicity of Staphylococcus aureus (S. aureus). In this study, effective Stp1 inhibitors were screened via virtual screening and enzyme activity experiments, and the inhibition mechanism was analyzed using molecular dynamics simulation. METHODS AutoDock Vina 4.0 software was used for virtual screening. The molecular structures of Stp1 and ligands were obtained from the RCSB Protein Data Bank and Zinc database, respectively. The molecular dynamics simulation used the Gromacs 4.5.5 software package with the Amberff99sb force field and TIP3P water model. AutoDock Tools was used to add polar hydrogen atoms to Stp1 and distribute part of the charge generated by Kollman's combined atoms. The binding free energies were calculated using the Amber 10 package. RESULTS The theoretical calculation results are consistent with the experimental results. We found that echinacoside (ECH) substantially inhibits the hydrolytic activity of Stp1. ECH competes with the substrate by binding to the active center of Stp1, resulting in a decrease in Stp1 activity. In addition, Met39, Gly41, Asp120, Asn162, and Ile163 were identified to play key roles in the binding of Stp1 to ECH. The benzene ring of ECH also plays an important role in complex binding. These findings provide a robust foundation for the development of innovative anti-infection drugs.
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Affiliation(s)
- Peng Xie
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Yue Gao
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Chenqi Wu
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Xuenan Li
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Yanan Yang
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China.
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Khan A, Sohail S, Yaseen S, Fatima S, Wisal A, Ahmed S, Nasir M, Irfan M, Karim A, Basharat Z, Khan Y, Aurongzeb M, Raza SK, Alshahrani MY, Morel CM, Hassan SS. Exploring and targeting potential druggable antimicrobial resistance targets ArgS, SecY, and MurA in Staphylococcus sciuri with TCM inhibitors through a subtractive genomics strategy. Funct Integr Genomics 2023; 23:254. [PMID: 37495774 DOI: 10.1007/s10142-023-01179-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023]
Abstract
Staphylococcus sciuri (also currently Mammaliicoccus sciuri) are anaerobic facultative and non-motile bacteria that cause significant human pathogenesis such as endocarditis, wound infections, peritonitis, UTI, and septic shock. Methicillin-resistant S. sciuri (MRSS) strains also infects animals that include healthy broilers, cattle, dogs, and pigs. The emergence of MRSS strains thereby poses a serious health threat and thrives the scientific community towards novel treatment options. Herein, we investigated the druggable genome of S. sciuri by employing subtractive genomics that resulted in seven genes/proteins where only three of them were predicted as final targets. Further mining the literature showed that the ArgS (WP_058610923), SecY (WP_058611897), and MurA (WP_058612677) are involved in the multi-drug resistance phenomenon. After constructing and verifying the 3D protein homology models, a screening process was carried out using a library of Traditional Chinese Medicine compounds (consisting of 36,043 compounds). The molecular docking and simulation studies revealed the physicochemical stability parameters of the docked TCM inhibitors in the druggable cavities of each protein target by identifying their druggability potential and maximum hydrogen bonding interactions. The simulated receptor-ligand complexes showed the conformational changes and stability index of the secondary structure elements. The root mean square deviation (RMSD) graph showed fluctuations due to structural changes in the helix-coil-helix and beta-turn-beta changes at specific points where the pattern of the RMSD and root mean square fluctuation (RMSF) (< 1.0 Å) support any major domain shifts within the structural framework of the protein-ligand complex and placement of ligand was well complemented within the binding site. The β-factor values demonstrated instability at few points while the radius of gyration for structural compactness as a time function for the 100-ns simulation of protein-ligand complexes showed favorable average values and denoted the stability of all complexes. It is assumed that such findings might facilitate researchers to robustly discover and develop effective therapeutics against S. sciuri alongside other enteric infections.
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Affiliation(s)
- Aafareen Khan
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000, KP, Pakistan
| | - Saman Sohail
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000, KP, Pakistan
| | - Seerat Yaseen
- Abbasi Shaheed Hospital, Karachi Medical and Dental College, Karachi, Pakistan
| | - Sareen Fatima
- Department of Microbiology, University of Balochistan, Quetta, Balochistan, Pakistan
| | - Ayesha Wisal
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000, KP, Pakistan
| | - Sufyan Ahmed
- Abbasi Shaheed Hospital, Karachi Medical and Dental College, Karachi, Pakistan
| | - Mahrukh Nasir
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Irfan
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Asad Karim
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Zarrin Basharat
- Alpha Genomics (Private) Limited, Islamabad, 44710, Pakistan
| | - Yasmin Khan
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Aurongzeb
- Faculty of Engineering Sciences & Technology, Hamdard University, Karachi, 74600, Pakistan
| | - Syed Kashif Raza
- Faculty of Rehabilitation and Allied Health Sciences (FRAHS), Riphah International University, Faisalabad, Pakistan
| | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha, 9088, Saudi Arabia
| | - Carlos M Morel
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building "Expansão", 8Th Floor Room 814, Av. Brasil 4036 - Manguinhos, Rio de Janeiro, RJ, 21040-361, Brazil.
| | - Syed S Hassan
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan.
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building "Expansão", 8Th Floor Room 814, Av. Brasil 4036 - Manguinhos, Rio de Janeiro, RJ, 21040-361, Brazil.
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Siddiqui S, Riaz S, Ahmad R, Wani MJ, Hashmi MA, Zofair SFF, Mateen S, Moin S. Synergistic effect of chlorogenic acid and vitamin D3 (cholecalciferol) on in-vitro glycation may assist in prevention of polycystic ovarian syndrome (PCOS) progression - A biophysical, biochemical and in-silico study. Int J Biol Macromol 2023; 245:125497. [PMID: 37369258 DOI: 10.1016/j.ijbiomac.2023.125497] [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: 03/26/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
Advanced glycation end products (AGEs) are formed through non-enzymatic glycation, that have been linked to various diseases, including polycystic ovarian syndrome (PCOS) playing a critical role leading to secondary comorbidities such as diabetes-related problems, cardiovascular complications, infertility, etc. As a result, there has been a lot of research into AGE-inhibiting phytochemicals for the remediation and obstruct progression of glycation-related illnesses. The current study is based on in-vitro protein model, in which human serum albumin have been used to investigate the cumulative effect of chlorogenic acid (CGA) and cholecalciferol (vitamin D) on glycation and evaluate their inhibitory impact on AGEs production in the presence of methylglyoxal. Through the application of several biochemical and biophysical techniques, we were able to examine the synergistic impact of both the compounds on albumin structure and its biochemical properties during different stages of glycation. According to Nitro-blue tetrazolium assay results indicate that CGA and vitamin D inhibited fructosamine (early glycation product) production. Moreover, free thiol and lysine residues were significantly increased whereas protein carbonyl levels were significantly decreased. Additive effect of CGA and vitamin D were associated with reduced AGEs fluorescence and increased tryptophan and tyrosine fluorescence. Amadori-albumin after treatment showed some evidence of regaining its alpha-helicity as measured by far-UV CD spectrum. Furthermore, secondary structural alterations were confirmed by Fourier transform infrared spectroscopy (FTIR). ANS (1-anilinonaphthalene-8-sulfonic acid) fluorescence spectra also displayed less revelation of hydrophobic patches. Bilirubin binding capacity was also restored which showed functional recovery of HSA. The electrophoretic mobility was also restored which is portrayed by SDS-PAGE. Additionally, to predict the anti-aggregation potential of CGA and vitamin D, congo red assay and ThT fluorescence was performed which reveal low aggregate formation after treatment. These results corroborated with scanning electron microscopy and confocal microscopy. Docking and simulation results also reveal spontaneous binding of CGA and vitamin D on subdomain IIA of HSA favoring their binding thermodynamically. All the findings suggest that chlorogenic acid and cholecalciferol given in combination might help in prevention of PCOS progression and its related complications.
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Affiliation(s)
- Sana Siddiqui
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Sana Riaz
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Rizwan Ahmad
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Mohd Junaid Wani
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Science, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Syeda Fauzia Farheen Zofair
- Interdisciplinary Biotechnology Unit, Faculty of Life Science, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Somaiya Mateen
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Shagufta Moin
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India.
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Ribeiro R, Botelho FD, Pinto AMV, La Torre AMA, Almeida JSFD, LaPlante SR, Franca TCC, Veiga-Junior VF, Dos Santos MC. Molecular modeling study of natural products as potential bioactive compounds against SARS-CoV-2. J Mol Model 2023; 29:183. [PMID: 37212923 DOI: 10.1007/s00894-023-05586-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/09/2023] [Indexed: 05/23/2023]
Abstract
CONTEXT The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 infection and responsible for millions of victims worldwide, remains a significant threat to public health. Even after the development of vaccines, research interest in the emergence of new variants is still prominent. Currently, the focus is on the search for effective and safe drugs, given the limitations and side effects observed for the synthetic drugs administered so far. In this sense, bioactive natural products that are widely used in the pharmaceutical industry due to their effectiveness and low toxicity have emerged as potential options in the search for safe drugs against COVID-19. Following this line, we screened 10 bioactive compounds derived from cholesterol for molecules capable of interacting with the receptor-binding domain (RBD) of the spike protein from SARS-CoV-2 (SC2Spike), responsible for the virus's invasion of human cells. Rounds of docking followed by molecular dynamics simulations and binding energy calculations enabled the selection of three compounds worth being experimentally evaluated against SARS-CoV-2. METHODS The 3D structures of the cholesterol derivatives were prepared and optimized using the Spartan 08 software with the semi-empirical method PM3. They were then exported to the Molegro Virtual Docking (MVD®) software, where they were docked onto the RBD of a 3D structure of the SC2Spike protein that was imported from the Protein Data Bank (PDB). The best poses obtained from MVD® were subjected to rounds of molecular dynamics simulations using the GROMACS software, with the OPLS/AA force field. Frames from the MD simulation trajectories were used to calculate the ligand's free binding energies using the molecular mechanics - Poisson-Boltzmann surface area (MM-PBSA) method. All results were analyzed using the xmgrace and Visual Molecular Dynamics (VMD) software.
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Affiliation(s)
- Rayssa Ribeiro
- Department of Chemical Engineering, Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Fernanda D Botelho
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Amanda M V Pinto
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Antonia M A La Torre
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Joyce S F D Almeida
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Steven R LaPlante
- INRS, Centre Armand-Frappier Santé Biotechnologie 531, Boulevard Des Prairies, Laval, QC, Canada
| | - Tanos C C Franca
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
- INRS, Centre Armand-Frappier Santé Biotechnologie 531, Boulevard Des Prairies, Laval, QC, Canada
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Valdir F Veiga-Junior
- Department of Chemical Engineering, Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Marcelo C Dos Santos
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil.
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Hashmi HB, Farooq MA, Khan MH, Alshammari A, Aljasham AT, Rashid SA, Khan NR, Hashmi IB, Badar M, Mubarak MS. Collaterally Sensitive β-Lactam Drugs as an Effective Therapy against the Pre-Existing Methicillin Resistant Staphylococcus aureus (MRSA) Biofilms. Pharmaceuticals (Basel) 2023; 16:ph16050687. [PMID: 37242471 DOI: 10.3390/ph16050687] [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: 03/07/2023] [Revised: 04/01/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is among the leading causes of nosocomial infections and forms biofilms, which are difficult to eradicate because of their increasing resistance to antimicrobial agents. This is especially true for pre-existing biofilms. The current study focused on evaluating the efficacy of three β-lactam drugs, meropenem, piperacillin, and tazobactam, alone and in combination against the MRSA biofilms. When used individually, none of the drugs exhibited significant antibacterial activity against MRSA in a planktonic state. At the same time, the combination of meropenem, piperacillin, and tazobactam showed a 41.7 and 41.3% reduction in planktonic bacterial cell growth, respectively. These drugs were further assessed for biofilm inhibition and removal. The combination of meropenem, piperacillin, and tazobactam caused 44.3% biofilm inhibition, while the rest of the combinations did not show any significant effects. Results also revealed that piperacillin and tazobactam exhibited the best synergy against the pre-formed biofilm of MRSA, with 46% removal. However, adding meropenem to the piperacillin and tazobactam combination showed a slightly reduced activity towards the pre-formed biofilm of MRSA and removed 38.7% of it. Although the mechanism of synergism is not fully understood, our findings suggest that these three β-lactam drugs can be used in combination as very effective therapeutic agents for the treatment of pre-existing MRSA biofilms. The in vivo experiments on the antibiofilm activity of these drugs will pave the way for applying such synergistic combinations to clinics.
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Affiliation(s)
- Hamna Batool Hashmi
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan
| | - Muhammad Asad Farooq
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, East China Normal University, Shanghai 200062, China
| | - Muhammad Hashim Khan
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Alanoud T Aljasham
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Sheikh Abdur Rashid
- Nanocarriers Research Laboratory, Gomal Centre of Pharmaceutical Sciences, Faculty of Pharmacy, Gomal University, Dera Ismail Khan 29050, Pakistan
| | - Nauman Rahim Khan
- Department of Pharmacy, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Irum Batool Hashmi
- Department of Obstetrics and Gynecology, Gomal Medical College, Dera Ismail Khan 29050, Pakistan
| | - Muhammad Badar
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29050, Pakistan
| | - Mohammad S Mubarak
- Department of Chemistry, The University of Jordan, Amma 11942, Jordan
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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Altharawi A, Alossaimi MA, Alanazi MM, Alqahatani SM, Tahir Ul Qamar M. An integrated computational approach towards novel drugs discovery against polyketide synthase 13 thioesterase domain of Mycobacterium tuberculosis. Sci Rep 2023; 13:7014. [PMID: 37117557 PMCID: PMC10147368 DOI: 10.1038/s41598-023-34222-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/26/2023] [Indexed: 04/30/2023] Open
Abstract
The acquired drug resistance by Mycobacterium tuberculosis (M. tuberculosis) to antibiotics urges the need for developing novel anti-M. tuberculosis drugs that possess novel mechanism of action. Since traditional drug discovery is a labor-intensive and costly process, computer aided drug design is highly appreciated tool as it speeds up and lower the cost of drug development process. Herein, Asinex antibacterial compounds were virtually screened against thioesterase domain of Polyketide synthase 13, a unique enzyme that forms α-alkyl β-ketoesters as a direct precursor of mycolic acids which are essential components of the lipid-rich cell wall of M. tuberculosis. The study identified three drug-like compounds as the most promising leads; BBB_26582140, BBD_30878599 and BBC_29956160 with binding energy value of - 11.25 kcal/mol, - 9.87 kcal/mol and - 9.33 kcal/mol, respectively. The control molecule binding energy score is -9.25 kcal/mol. Also, the docked complexes were dynamically stable with maximum root mean square deviation (RMSD) value of 3 Å. Similarly, the MM-GB\PBSA method revealed highly stable complexes with mean energy values < - 75 kcal/mol for all three systems. The net binding energy scores are validated by WaterSwap and entropy energy analysis. Furthermore, The in silico druglike and pharmacokinetic investigation revealed that the compounds could be suitable candidates for additional experimentations. In summary, the study findings are significant, and the compounds may be used in experimental validation pipeline to develop potential drugs against drug-resistant tuberculosis.
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Affiliation(s)
- Ali Altharawi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Manal A Alossaimi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Mohammed M Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Safar M Alqahatani
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Muhammad Tahir Ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, 38000, Pakistan.
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Isolation and Characterization of Novel Hydroxyflavone from Kigelia africana (Lam.) Benth. Fruit Ethyl Acetate Fraction against CHO 1 and HeLa Cancer Cell Lines: In vitro and in silico studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Usmani J, Kausar H, Akbar S, Sartaj A, Mir SR, Hassan MJ, Sharma M, Ahmad R, Rashid S, Ansari MN. Molecular Docking of Bacterial Protein Modulators and Pharmacotherapeutics of Carica papaya Leaves as a Promising Therapy for Sepsis: Synchronising In Silico and In Vitro Studies. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020574. [PMID: 36677632 PMCID: PMC9862608 DOI: 10.3390/molecules28020574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 01/09/2023]
Abstract
Sepsis is a serious health concern globally, which necessitates understanding the root cause of infection for the prevention of proliferation inside the host's body. Phytochemicals present in plants exhibit antibacterial and anti-proliferative properties stipulated for sepsis treatment. The aim of the study was to determine the potential role of Carica papaya leaf extract for sepsis treatment in silico and in vitro. We selected two phytochemical compounds, carpaine and quercetin, and docked them with bacterial proteins, heat shock protein (PDB ID: 4PO2), surfactant protein D (PDB ID: 1PW9), and lactobacillus bacterial protein (PDB ID: 4MKS) against imipenem and cyclophosphamide. Quercetin showed the strongest interaction with 1PW9 and 4MKS proteins. The leaves were extracted using ethanol, methanol, and water through Soxhlet extraction. Total flavonoid content, DPPH assay, HPTLC, and FTIR were performed. In vitro cytotoxicity of ethanol extract was screened via MTT assay on the J774 cell line. Ethanol extract (EE) possessed the maximum number of phytocomponents, the highest amount of flavonoid content, and the maximum antioxidant activity compared to other extracts. FTIR analysis confirmed the presence of N-H, O-H, C-H, C=O, C=C, and C-Cl functional groups in ethanol extract. Cell viability was highest (100%) at 25 µg/mL of EE. The present study demonstrated that the papaya leaves possessed antibacterial and cytotoxic activity against sepsis infection.
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Affiliation(s)
- Juveria Usmani
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard University, New Delhi 110062, India
| | - Hina Kausar
- Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard University, New Delhi 110062, India
| | - Saleem Akbar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard University, New Delhi 110062, India
| | - Ali Sartaj
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard University, New Delhi 110062, India
| | - Showkat R. Mir
- Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard University, New Delhi 110062, India
| | - Mohammed Jaseem Hassan
- Department of Pathology, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh 202002, India
| | - Manju Sharma
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard University, New Delhi 110062, India
| | - Razi Ahmad
- Department of Pharmacology, Hamdard Institute of Medical Sciences and Research, Jamia Hamdard University, New Delhi 110062, India
- Correspondence: (R.A.); (M.N.A.)
| | - Summaya Rashid
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Mohd Nazam Ansari
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Correspondence: (R.A.); (M.N.A.)
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