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Khan MU, Sakhawat A, Rehman R, Wali AH, Ghani MU, Akram A, Javed MA, Ali Q, Yu-Ming Z, Ali D, Yu-Ming Z. Identification of novel natural compounds against CFTR p.Gly628Arg pathogenic variant. AMB Express 2024; 14:99. [PMID: 39249658 PMCID: PMC11383896 DOI: 10.1186/s13568-024-01762-9] [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: 06/20/2024] [Accepted: 08/27/2024] [Indexed: 09/10/2024] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) protein is an ion channel found in numerous epithelia and controls the flow of water and salt across the epithelium. The aim of our study to find natural compounds that can improve lung function for people with cystic fibrosis (CF) caused by the p.Gly628Arg (rs397508316) mutation of CFTR protein. The sequence of CFTR protein as a target structure was retrieved from UniProt and PDB database. The ligands that included Armepavine, Osthole, Curcumin, Plumbagine, Quercetin, and one Trikafta (R*) reference drug were screened out from PubChem database. Autodock vina software carried out docking, and binding energies between the drug and the target were included using docking-score. The following tools examined binding energy, interaction, stability, toxicity, and visualize protein-ligand complexes. The compounds having binding energies of -6.4, -5.1, -6.6, -5.1, and - 6.5 kcal/mol for Armepavine, Osthole, Curcumin, Plumbagine, Quercetin, and R*-drug, respectively with mutated CFTR (Gly628Arg) structure were chosen as the most promising ligands. The ligands bind to the mutated CFTR protein structure active sites in hydrophobic bonds, hydrogen bonds, and electrostatic interactions. According to ADMET analyses, the ligands Armepavine and Quercetin also displayed good pharmacokinetic and toxicity characteristics. An MD simulation for 200 ns was also established to ensure that Armepavine and Quercetin ligands attached to the target protein favorably and dynamically, and that protein-ligand complex stability was maintained. It is concluded that Armepavine and Quercetin have stronger capacity to inhibit the effect of mutated CFTR protein through improved trafficking and restoration of original function.
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Affiliation(s)
- Muhammad Umer Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.
| | - Azra Sakhawat
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Raima Rehman
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Abbas Haider Wali
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Usman Ghani
- Precision Genomics Research Lab, Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Areeba Akram
- Precision Genomics Research Lab, Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
| | - Zhou Yu-Ming
- Department of Emergency, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, 341000, Jiangxi Province, P.R. China
| | - Daoud Ali
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
| | - Zhou Yu-Ming
- Department of Emergency, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, 341000, Jiangxi Province, P.R. China
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Vaccarin C, Veit G, Hegedus T, Torres O, Chilin A, Lukacs GL, Marzaro G. Synthesis and Biological Evaluation of Pyrazole-Pyrimidones as a New Class of Correctors of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). J Med Chem 2024; 67:13891-13908. [PMID: 39137389 DOI: 10.1021/acs.jmedchem.4c00685] [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: 08/15/2024]
Abstract
Cystic fibrosis (CF) is caused by the functional expression defect of the cystic fibrosis transmembrane conductance regulator (CFTR) protein. Despite the recent success in CFTR modulator development, the available correctors only partially restore the F508del-CFTR channel function, and several rare CF mutations show resistance to available drugs. We previously identified compound 4172 that synergistically rescued the F508del-CFTR folding defect in combination with the existing corrector drugs VX-809 and VX-661. Here, novel CFTR correctors were designed by applying a classical medicinal chemistry approach on the 4172 scaffold. Molecular docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were conducted to propose a plausible binding site and design more potent and effective analogs. We identified three optimized compounds, which, in combination with VX-809 and the investigational corrector 3151, increased the plasma membrane density and function of F508del-CFTR and other rare CFTR mutants resistant to the currently approved therapies.
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Affiliation(s)
- Christian Vaccarin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
- Center for Radiopharmaceutical Sciences, ETH-PSI-USZ, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Guido Veit
- Department of Physiology and Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Tamas Hegedus
- Institute of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
- HUN-REN Biophysical Virology Research Group, Hungarian Research Network, Budapest 1052, Hungary
| | - Odalys Torres
- Institute of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
| | - Adriana Chilin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Gergely L Lukacs
- Department of Physiology and Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Giovanni Marzaro
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
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Fundamentals of HDX-MS. Essays Biochem 2022; 67:301-314. [PMID: 36251047 PMCID: PMC10070489 DOI: 10.1042/ebc20220111] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is becoming part of the standard repertoire of techniques used by molecular biologists to investigate protein structure and dynamics. This is partly due to the increased use of automation in all stages of the technique and its versatility of application-many proteins that present challenges with techniques such as X-ray crystallography and cryoelectron microscopy are amenable to investigation with HDX-MS. The present review is aimed at scientists who are curious about the technique, and how it may aid their research. It describes the fundamental basis of solvent exchange, the basics of a standard HDX-MS experiment, as well as highlighting emerging novel experimental advances, which point to where the field is heading.
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