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Wang X, Sun J, Nie Z, Ma L, Sai H, Cheng J, Liu Y, Duan J. Effect of Chloramphenicol as Antibiotic on the Structure and Function of Pepsin and Its Mechanism of Action. Chem Biodivers 2024; 21:e202301554. [PMID: 38128109 DOI: 10.1002/cbdv.202301554] [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: 10/03/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023]
Abstract
The interaction between chloramphenicol (CHL) and pepsin (PEP), as well as the impact of CHL on PEP conformation, were investigated using spectroscopic techniques and molecular docking simulations in this study. The experimental results demonstrate that CHL exhibits a static quenching effect on PEP. The thermodynamic parameters indicate that the reaction between CHL and PEP is spontaneous, primarily driven by hydrogen bonding and van der Waals forces. Moreover, the binding distance of r<7 nm suggests the occurrence of Förster's non-radiative energy transfer between these two molecules. In the synchronous fluorescence spectrum, the maximum fluorescence intensity of PEP produced a redshift phenomenon, indicating that CHL was bound to tryptophan residues of PEP. The addition of CHL induces changes in the secondary structure of PEP, as confirmed by the observed alterations in peak values in three-dimensional fluorescence spectra. The UV spectra reveal a redshift of 3 nm in the maximum absorption peak, indicating a conformational change in the secondary structure of PEP upon addition of CHL. Circular dichroism analysis demonstrates significant alterations in the α-helix, β-sheet, β-turn, and random coil contents of PEP before and after CHL incorporation, further confirming its ability to modulate the secondary structure of PEP.
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Affiliation(s)
- Xiaoxia Wang
- School of Chemistry and Chemical Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China
- Innermongolia Engineering Research Center of Comprehensive Utilization of Bio-coal Chemical Industry, Baotou, 014010, China
| | - Jisheng Sun
- School of Chemistry and Chemical Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Zhihua Nie
- School of life sciences, Tsinghua University, Beijing, 100084, China
| | - Litong Ma
- School of Chemistry and Chemical Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China
- Innermongolia Engineering Research Center of Comprehensive Utilization of Bio-coal Chemical Industry, Baotou, 014010, China
| | - Huazheng Sai
- School of Chemistry and Chemical Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Jianguo Cheng
- School of Chemistry and Chemical Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Yunying Liu
- School of Chemistry and Chemical Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Jianguo Duan
- School of Chemistry and Chemical Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China
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Metwally K, Abo-Dya NE, Hamdan AME, Alrashidi MN, Alturki MS, Aly OM, Aljoundi A, Ibrahim M, Soliman MES. Investigation of Simultaneous and Sequential Cooperative Homotropic Inhibitor Binding to the Catalytic Chamber of SARS-CoV-2 RNA-dependent RNA Polymerase (RdRp). Cell Biochem Biophys 2023; 81:697-706. [PMID: 37658974 DOI: 10.1007/s12013-023-01163-y] [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] [Accepted: 08/05/2023] [Indexed: 09/05/2023]
Abstract
In our previous report, the unique architecture of the catalytic chamber of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), which harbours two distinctive binding sites, was fully characterized at molecular level. The significant differences in the two binding sites BS1 and BS2 in terms of binding pockets motif, as well as the preferential affinities of eight anti-viral drugs to each of the two binding sites were described. Recent Cryogenic Electron Microscopy (Cryo-EM) studies on the RdRp revealed that two suramin molecules, a SARS-CoV-2 inhibitor, bind to RdRp in two different sites with distinctive interaction landscape. Here, we provide the first account of investigating the combined inhibitor binding to both binding sites, and whether the binding of two inhibitors molecules concurrently is "Cooperative binding" or not. It should be noted that the binding of inhibitors to different sites do not necessary constitute mutually independent events, therefore, we investigated two scenarios to better understand cooperativity: simultaneous binding and sequential binding. It has been demonstrated by binding free energy calculations (MM/PBSA) and piecewise linear potential (PLP) interaction energy analysis that the co-binding of two suramin molecules is not cooperative in nature; rather, when compared to individual binding, both molecules adversely affect one another's binding affinities. This observation appeared to be primarily due to RdRp's rigidity, which prevented both ligands from fitting comfortably within the catalytic chamber. Instead, the suramin molecules showed a tendency to change their orientation within the binding pockets in order to maintain their binding to the protein, but at the expense of the ligand internal energies. Although co-binding resulted in the loss of several important key interactions, a few interactions were conserved, and these appear to be crucial in preserving the binding of ligands in the active site. The structural and mechanistic details of this study will be useful for future research on creating and developing RdRp inhibitors against SARS-CoV-2.
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Affiliation(s)
- Kamel Metwally
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk, 71491, Saudi Arabia.
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt.
| | - Nader E Abo-Dya
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk, 71491, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt
| | - Ahmed M E Hamdan
- Department of Pharmacy Practice, Faculty of Pharmacy, University of Tabuk, Tabuk, 71491, Saudi Arabia
| | - Maram N Alrashidi
- Pharm D Program, Faculty of Pharmacy, University of Tabuk, Tabuk, 71491, Saudi Arabia
| | - Mansour S Alturki
- Department of Pharmaceutical Chemistry, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam, 34212, Saudi Arabia
| | - Omar M Aly
- Medicinal Chemistry Department Faculty of Pharmacy Port Said University, Port Said, 42526, Egypt
| | - Aimen Aljoundi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud Ibrahim
- CompChem Lab, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
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Mustafa SK, Jame R, Aljohani MMH, Omer N, Alessa AH, Al-Anazi M, Alotaibi FA, Sk M, Islam M, Shakya S. Synthesis, spectrophotometric, pharmacology and theoretical investigation of a new electron transfer complex of 8-hydroxyquinoline with oxalic acid in different polar solvents. J Biomol Struct Dyn 2023:1-13. [PMID: 37962847 DOI: 10.1080/07391102.2023.2279277] [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: 07/13/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023]
Abstract
Preparation, characterization, and investigation of a novel organic charge transfer (CT) complex were carried out, with a focus on exploring its antibacterial and antifungal characteristics. Theoretical analysis backs up the experimental findings. CT complex formed was synthesized between 8-hydroxyquinoline (8HQ) and oxalic acid (OA) at RT (room temperature). Different analyses were used to describe the CT complex, including 1H-NMR, FTIR, TGA/DTA, and UV-vis spectra (in different solvents). These indicate that the CT interaction is linked to proton transfer from OA to 8HQ and the subsequent development of 'N+__H…O-" type bonding. On the basis of wave number, the CT complex and reactants are distinguished in FTIR spectra. By using Thermo gravimetric Analysis/Differential Thermal Analysis (TGA/DTA) tests, the thermal stability of complicated and thorough corrosion was examined. Through UV-visible spectroscopy, physical characteristics like ECT (interaction energy), RN (resonance energy), ID (ionization potential), f (oscillator strength) and ΔG (free energy) were calculated. The εCT (molar extinction coefficient), the KCT (formation constant), and additional physical properties of this complex were calculated by the Benesi-Hildebrand equation in order to determine its 1:1 stoichiometry. The biological properties are also supported by theoretical study. The protein, Human Serum Albumin (HSA), is observed to bind with CT complex, as shown by molecular docking and the observed binding energy value is -167.04 kcal/mol. Molecular dynamics (MD) simulation 100 ns run was used to refine docking results and binding free energy was calculated using MM-PBSA. This study introduces a novel CT complex, offering fresh perspectives on molecular interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Syed Khalid Mustafa
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Rasha Jame
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Meshari M H Aljohani
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Noha Omer
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Ali Hamzah Alessa
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Menier Al-Anazi
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Fatimah A Alotaibi
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Matiur Sk
- Department of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh, India
| | - Maidul Islam
- Department of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh, India
| | - Sonam Shakya
- Department of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh, India
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Metwally K, Abo-Dya NE, Alahmdi MI, Albalawi MZ, Yahya G, Aljoundi A, Salifu EY, Elamin G, Ibrahim MAA, Sayed Y, Fanucchi S, Soliman MES. The Unusual Architecture of RNA-Dependent RNA Polymerase (RdRp)'s Catalytic Chamber Provides a Potential Strategy for Combination Therapy against COVID-19. Molecules 2023; 28:molecules28062806. [PMID: 36985777 PMCID: PMC10057333 DOI: 10.3390/molecules28062806] [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: 02/21/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The unusual and interesting architecture of the catalytic chamber of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) was recently explored using Cryogenic Electron Microscopy (Cryo-EM), which revealed the presence of two distinctive binding cavities within the catalytic chamber. In this report, first, we mapped out and fully characterized the variations between the two binding sites, BS1 and BS2, for significant differences in their amino acid architecture, size, volume, and hydrophobicity. This was followed by investigating the preferential binding of eight antiviral agents to each of the two binding sites, BS1 and BS2, to understand the fundamental factors that govern the preferential binding of each drug to each binding site. Results showed that, in general, hydrophobic drugs, such as remdesivir and sofosbuvir, bind better to both binding sites than relatively less hydrophobic drugs, such as alovudine, molnupiravir, zidovudine, favilavir, and ribavirin. However, suramin, which is a highly hydrophobic drug, unexpectedly showed overall weaker binding affinities in both binding sites when compared to other drugs. This unexpected observation may be attributed to its high binding solvation energy, which disfavors overall binding of suramin in both binding sites. On the other hand, hydrophobic drugs displayed higher binding affinities towards BS1 due to its higher hydrophobic architecture when compared to BS2, while less hydrophobic drugs did not show a significant difference in binding affinities in both binding sites. Analysis of binding energy contributions revealed that the most favorable components are the ΔEele, ΔEvdw, and ΔGgas, whereas ΔGsol was unfavorable. The ΔEele and ΔGgas for hydrophobic drugs were enough to balance the unfavorable ΔGsol, leaving the ΔEvdw to be the most determining factor of the total binding energy. The information presented in this report will provide guidelines for tailoring SARS-CoV-2 inhibitors with enhanced binding profiles.
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Affiliation(s)
- Kamel Metwally
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Nader E Abo-Dya
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Mohammed Issa Alahmdi
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Maha Z Albalawi
- Pharm D Program, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Aimen Aljoundi
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Elliasu Y Salifu
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Ghazi Elamin
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud A A Ibrahim
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
- CompChem Lab, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Sylvia Fanucchi
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
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Gaber A, Alsanie WF, Alhomrani M, Alamri AS, Alyami H, Shakya S, Habeeballah H, Alkhatabi HA, Felimban RI, Alamri A, Alhabeeb AA, Raafat BM, Refat MS. Multispectral and Molecular Docking Studies Reveal Potential Effectiveness of Antidepressant Fluoxetine by Forming π-Acceptor Complexes. Molecules 2022; 27:molecules27185883. [PMID: 36144618 PMCID: PMC9505585 DOI: 10.3390/molecules27185883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022] Open
Abstract
Poor mood, lack of pleasure, reduced focus, remorse, unpleasant thoughts, and sleep difficulties are all symptoms of depression. The only approved treatment for children and adolescents with major depressive disorder (MDD) is fluoxetine hydrochloride (FXN), a serotonin selective reuptake inhibitor antidepressant. MDD is the most common cause of disability worldwide. In the present research, picric acid (PA); dinitrobenzene; p-nitro benzoic acid; 2,6-dichloroquinone-4-chloroimide; 2,6-dibromoquinone-4-chloroimide; and 7,7′,8,8′-tetracyanoquinodimethane were used to make 1:1 FXN charge-transfer compounds in solid and liquid forms. The isolated complexes were then characterized by elemental analysis, conductivity, infrared, Raman, and 1H-NMR spectra, thermogravimetric analysis, scanning electron microscopy, and X-ray powder diffraction. Additionally, a molecular docking investigation was conducted on the donor moiety using FXN alone and the resulting charge transfer complex [(FXN)(PA)] as an acceptor to examine the interactions against two protein receptors (serotonin or dopamine). Interestingly, the [(FXN)(PA)] complex binds to both serotonin and dopamine more effectively than the FXN drug alone. Furthermore, [(FXN)(PA)]–serotonin had a greater binding energy than [FXN]–serotonin. Theoretical data were also generated by density functional theory simulations, which aided the molecular geometry investigation and could be beneficial to researchers in the future.
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Affiliation(s)
- Ahmed Gaber
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Correspondence: (A.G.); (M.S.R.)
| | - Walaa F. Alsanie
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Department of Clinical Laboratories Sciences, The Faculty of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Majid Alhomrani
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Department of Clinical Laboratories Sciences, The Faculty of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Abdulhakeem S. Alamri
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Department of Clinical Laboratories Sciences, The Faculty of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Hussain Alyami
- College of Medicine, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Sonam Shakya
- Department of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh 202002, India
| | - Hamza Habeeballah
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences in Rabigh, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Heba A. Alkhatabi
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- King Fahd Medical Research Centre, Hematology Research Unit, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Raed I. Felimban
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Center of Innovation in Personalized Medicine (CIPM), 3D Bioprinting Unit, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Abdulwahab Alamri
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Hail, P.O. Box 2240, Hail 55476, Saudi Arabia
| | | | - Bassem M. Raafat
- Department of Radiological Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Moamen S. Refat
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Correspondence: (A.G.); (M.S.R.)
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