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Nawaz MZ, Khalid HR, Shahbaz S, Al-Ghanim KA, Pugazhendhi A, Zhu D. Discovery of putative inhibitors of human Pkd1 enzyme: Molecular docking, dynamics and simulation, QSAR, and MM/GBSA. ENVIRONMENTAL RESEARCH 2024; 257:119336. [PMID: 38838751 DOI: 10.1016/j.envres.2024.119336] [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: 12/26/2023] [Revised: 05/08/2024] [Accepted: 06/02/2024] [Indexed: 06/07/2024]
Abstract
Polycystic kidney disease is the most prevalent hereditary kidney disease globally and is mainly linked to the overexpression of a gene called PKD1. To date, there is no effective treatment available for polycystic kidney disease, and the practicing treatments only provide symptomatic relief. Discovery of the compounds targeting the PKD1 gene by inhibiting its expression under the disease condition could be crucial for effective drug development. In this study, a molecular docking and molecular dynamic simulation, QSAR, and MM/GBSA-based approaches were used to determine the putative inhibitors of the Pkd1 enzyme from a library of 1379 compounds. Initially, fourteen compounds were selected based on their binding affinities with the Pkd1 enzyme using MOE and AutoDock tools. The selected drugs were further investigated to explore their properties as drug candidates and the stability of their complex formation with the Pkd1 enzyme. Based on the physicochemical and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties, and toxicity profiling, two compounds including olsalazine and diosmetin were selected for the downstream analysis as they demonstrated the best drug-likeness properties and highest binding affinity with Pkd1 in the docking experiment. Molecular dynamic simulation using Gromacs further confirmed the stability of olsalazine and diosmetin complexes with Pkd1 and establishing interaction through strong bonding with specific residues of protein. High biological activity and binding free energies of two complexes calculated using 3D QSAR and Schrodinger module, respectively further validated our results. Therefore, the molecular docking and dynamics simulation-based in-silico approach used in this study revealed olsalazine and diosmetin as potential drug candidates to combat polycystic kidney disease by targeting Pkd1 enzyme.
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Affiliation(s)
- Muhammad Zohaib Nawaz
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Hafiz Rameez Khalid
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Sabeen Shahbaz
- Department of Biochemistry, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Khalid A Al-Ghanim
- Department of Zoology, College of Science, King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia
| | - Arivalagan Pugazhendhi
- School of Engineering, Lebanese American University, Byblos, Lebanon; University Centre for Research & Development, Department of Civil Engineering, Chandigarh University, Mohali, 140103, India.
| | - Daochen Zhu
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
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Paulraj MS, Eringathodi S, Mollah AKMM, Alexis Thayaparan CT, Kuldeep SA, Subramanian PS, M I, Dhanaraj P. 2-[( E)-(2-carboxybenzylidene) amino] ethan ammonium-like amino acid zwitterions: crystal structure, functional studies and its molecular dynamic simulation study with drug target receptors. J Biomol Struct Dyn 2024; 42:6081-6090. [PMID: 37403277 DOI: 10.1080/07391102.2023.2230296] [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: 11/22/2022] [Accepted: 06/22/2023] [Indexed: 07/06/2023]
Abstract
The novel synthetic amino acid-like zwitterion containing imine bond ionic compound 2-[(E)-(2-carboxy benzylidene) amino] ethan ammonium salt, C10H12N2O2, was synthesized. Computational functional characterization is now being used to predict novel compounds. Here, we report on a titled combination that has been crystallizing in orthorhombic space group Pcc2 with Z = 4. The zwitterions form centrosymmetric dimers to polymeric supramolecular network via intermolecular N-H… O hydrogen bonds between the carboxylate groups and ammonium ion. The components are linked by ionic (N+-H-O-) and hydrogen bonds (N+-H-O), forming a complex three-dimensional supramolecular network. Further, molecular computational docking characterization study was performed with compound against multi-disease drug target biomolecule of anticancer target molecule of HDAC8 (PDB ID 1T69) receptor and antiviral molecular target protease (PDB ID 6LU7) to evaluate the interaction stability, conformational changes and to get insights into the natural dynamics on different timescales in solution. HighlightsThe novel zwitter ionic amino acid compound 2-[(E)-(2-carboxybenzylidene) amino] ethan ammonium salt, C10H12N2O2.The crystal structure determined for this compound illustrates the presence of intermolecular ionic N+-H-O- and N+-H-O hydrogen bonds between the carboxylate groups and ammonium ion, which influence the formation of a complex three-dimensional supramolecular polymeric network.Molecular docking studies helps to understand the conformational stability and interaction stabilityThe novel molecule can be considered for anticancer treatment.
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Affiliation(s)
| | - Suresh Eringathodi
- Analytical and Environmental Science Division and Centralized Instrument Facility, CSIR - Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
| | | | | | | | - Palani Sivagnana Subramanian
- Inorganic Materials and Catalysis Division, CSIR - Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
| | - Indiraleka M
- Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi, Tamil Nadu, India
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Satapathy S, Kumar S, Kurmi BD, Gupta GD, Patel P. Expanding the Role of Chiral Drugs and Chiral Nanomaterials as a Potential Therapeutic Tool. Chirality 2024; 36:e23698. [PMID: 38961803 DOI: 10.1002/chir.23698] [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: 10/19/2023] [Revised: 05/08/2024] [Accepted: 05/31/2024] [Indexed: 07/05/2024]
Abstract
Chirality, the property of molecules having mirror-image forms, plays a crucial role in pharmaceutical and biomedical research. This review highlights its growing importance, emphasizing how chiral drugs and nanomaterials impact drug effectiveness, safety, and diagnostics. Chiral molecules serve as precise diagnostic tools, aiding in accurate disease detection through unique biomolecule interactions. The article extensively covers chiral drug applications in treating cardiovascular diseases, CNS disorders, local anesthesia, anti-inflammatories, antimicrobials, and anticancer drugs. Additionally, it explores the emerging field of chiral nanomaterials, highlighting their suitability for biomedical applications in diagnostics and therapeutics, enhancing medical treatments.
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Affiliation(s)
- Sourabh Satapathy
- Department of Pharmaceutical Chemistry and Analysis, ISF College of Pharmacy, Moga, Punjab, India
| | - Shivam Kumar
- Department of Pharmaceutical Chemistry and Analysis, ISF College of Pharmacy, Moga, Punjab, India
| | - Balak Das Kurmi
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
| | | | - Preeti Patel
- Department of Pharmaceutical Chemistry and Analysis, ISF College of Pharmacy, Moga, Punjab, India
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Nisar H, Attique SA, Javaid A, Ain QU, Butt F, Zaid M, Shahid S, Hassan Nasir M, Sadaf S. Comparative molecular docking analysis for analyzing the inhibitory effect of Anakinra and Ustekinumab against IL17F. J Biomol Struct Dyn 2023; 41:13302-13313. [PMID: 36715128 DOI: 10.1080/07391102.2023.2173299] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/19/2023] [Indexed: 01/31/2023]
Abstract
Interleukin 17 F is a member of IL-17 cytokine family with a 50% structural homology to IL-17A and plays a significant role either alone or in combination with IL-17A towards inflammation in Rheumatoid arthritis (RA). A growing number of drugs targeting IL-17 pathway are being tested against population specific disease markers. The major objective of this research was to investigate the anti-inflammatory effect of Anakinra (an IL-1 R1 inhibitor) and Ustekinumab (an IL-12 and IL-23 inhibitor) by targeting IL17F. The three dimensional structures of IL17F was taken from PDB while structures of drugs were taken from PubChem database. Docking was performed using MOE and Schrodinger ligand docking software and binding energies, including s-score using London-dG fitness function and glide score using glide internal energy function, between drug and targets were compared. Furthermore, Protein-Drug complex were subjected to 150 ns Molecular Dynamics (MD) Simulations using Schrodinger's Desmond Module. Docking and MD simulation results suggest anakinra as a more potent IL17F inhibitor and forming a more structurally stable complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Haseeb Nisar
- Department of Life-Sciences, University of Management and Technology, Lahore, Pakistan
| | - Syed Awais Attique
- School of Interdisciplinary Engineering & Science (SINES), National University of Sciences & Technology (NUST), Islamabad, Pakistan
| | - Anum Javaid
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Qurat Ul Ain
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- Department of Forensic sciences, Faculty of Medicine and Allied Health Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Fatima Butt
- Department of Life-Sciences, University of Management and Technology, Lahore, Pakistan
| | - Muhammad Zaid
- Department of Life-Sciences, University of Management and Technology, Lahore, Pakistan
| | - Samiah Shahid
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Hassan Nasir
- Faculty of Medicine, University Sultan Zainul Abidin, Jalal Sultan Mahmood, Malaysia
| | - Saima Sadaf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
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Molecular Modeling Guided Drug Designing for the Therapeutic Treatment of Rheumatoid Arthritis. Cell Microbiol 2022. [DOI: 10.1155/2022/7360782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Rheumatoid arthritis (RA) is a systemic inflammatory disorder that can cause destructive joint disease, significant disability, and increased mortality. RA is the most frequent of all chronic inflammatory joint diseases, and its prevalence frequency in Pakistan is 1.6 per thousand people. Different cytokines and receptors were involved in the triggering of RA, including interleukin-6 (ILR-6), major histocompatibility complex (MHC) antigen human leukocyte (HLA-DR) receptor, and CD20. Several studies illustrated RA as an inherent immune response and triggered due to the “shared epitope.” Therefore, the involvement of all these receptors (IL-6, HLA-DR, and CD20) leads to the neurological, ocular, respiratory, cardiac, skin, and hematological manifestations that have been considered a potential therapeutic target for drug design. Various herbal, natural, and synthetic source inhibitors of interleukin-6 (IL-6), human leukocyte (HLA-DR), and CD20 were studied and reported previously. Reported inhibitors are compared to elucidate the best inhibitor for clinical trials, leading to the orally active drug. In this study, a computer-aided drug designing approach disclosed the potential inhibitors for all receptors based on their distinct binding affinity. Moreover, drug suitability was carried out using Lipinski’s rule by considering the adsorption, distribution, metabolism, and excretion (ADME) of ligands. Results elucidated “calycosin 7-O-glucoside” and “angeliferulate” as putative ligands for IL-6 and HLA-DR, respectively. However, the pharmacokinetic properties (ADMET) revealed angeliferulate as an effete ligand for the biological system compared to calycosin 7-O-glucoside. Based on docking, drug toxicity profiling or pharmacokinetics, and MD simulation stability, this study highlights orally active therapeutic inhibitors to inhibit the activity of pivotal receptors (IL6, HLA-DR, and CD20) of RA in humans. After clinical trials, the resultant inhibitors could be potential therapeutic agents in the drug development against RA.
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Scope of repurposed drugs against the potential targets of the latest variants of SARS-CoV-2. Struct Chem 2022; 33:1585-1608. [PMID: 35938064 PMCID: PMC9346052 DOI: 10.1007/s11224-022-02020-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/19/2022] [Indexed: 11/21/2022]
Abstract
The unprecedented outbreak of the severe acute respiratory syndrome (SARS) Coronavirus-2, across the globe, triggered a worldwide uproar in the search for immediate treatment strategies. With no specific drug and not much data available, alternative approaches such as drug repurposing came to the limelight. To date, extensive research on the repositioning of drugs has led to the identification of numerous drugs against various important protein targets of the coronavirus strains, with hopes of the drugs working against the major variants of concerns (alpha, beta, gamma, delta, omicron) of the virus. Advancements in computational sciences have led to improved scope of repurposing via techniques such as structure-based approaches including molecular docking, molecular dynamic simulations and quantitative structure activity relationships, network-based approaches, and artificial intelligence-based approaches with other core machine and deep learning algorithms. This review highlights the various approaches to repurposing drugs from a computational biological perspective, with various mechanisms of action of the drugs against some of the major protein targets of SARS-CoV-2. Additionally, clinical trials data on potential COVID-19 repurposed drugs are also highlighted with stress on the major SARS-CoV-2 targets and the structural effect of variants on these targets. The interaction modelling of some important repurposed drugs has also been elucidated. Furthermore, the merits and demerits of drug repurposing are also discussed, with a focus on the scope and applications of the latest advancements in repurposing.
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Nawaz MZ, Attique SA, Ain QU, Alghamdi HA, Bilal M, Yan W, Zhu D. Discovery and characterization of dual inhibitors of human Vanin-1 and Vanin-2 enzymes through molecular docking and dynamic simulation-based approach. Int J Biol Macromol 2022; 213:1088-1097. [PMID: 35697166 DOI: 10.1016/j.ijbiomac.2022.06.014] [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: 12/19/2021] [Revised: 05/24/2022] [Accepted: 06/05/2022] [Indexed: 12/14/2022]
Abstract
The vanins are ectoenzymes with pantetheinase activity and are involved in recycling pantothenic acid (vitamin B5) from pantetheine. Elevated levels of vanin have been linked with the development and severity of several diseases, including steatosis, diabetes, skin diseases, cancer, inflammatory diseases etc. Therefore, vanins have previously been used as a potential drug target to combat related diseases. In this study, we used a molecular docking and molecular dynamic simulation-based approach to screen dual inhibitors of hVnn1, and hVnn2 from a library of 120 chemical candidates. Molecular docking of drug candidates with hVnn1, and hVnn2 using GOLD and MOE revealed that the chemical compound "methotrexate (CID: 126941)" has the highest binding affinity against both the target enzymes which was further validated through molecular dynamic simulation. Toxicity profiling of drug candidates evaluated using Lipinski's rule of five and Molsoft tool, and AdmetSar 2.0 confirms the drug suitability of methotrexate, therefore, suggesting its use as a potential therapeutic agent to inhibit the activity of vainin enzyme in related disease conditions.
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Affiliation(s)
- Muhammad Zohaib Nawaz
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Department of Computer Science, University of Agriculture, Faisalabad 38040, Pakistan
| | - Syed Awais Attique
- Department of Computer Science, University of Agriculture, Faisalabad 38040, Pakistan
| | - Qurat-Ul Ain
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Huda Ahmed Alghamdi
- Department of Biology, College of Sciences, King Khalid University, Abha 61413, Saudi Arabia
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China.
| | - Wei Yan
- Department of Marine Science, College of Marine Science and Technology, China University of Geosciences, Wuhan, China
| | - Daochen Zhu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
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Muhammad S, Saba A, Khera RA, Al-Sehemi AG, Algarni H, Iqbal J, Alshahrani MY, Chaudhry AR. Virtual screening of potential inhibitor against breast cancer-causing estrogen receptor alpha (ERα): molecular docking and dynamic simulations. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2072840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Shabbir Muhammad
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
| | - Afsheen Saba
- Department of Chemistry, College of Science, University of Agriculture, Faisalabad, Pakistan
| | - Rasheed Ahmad Khera
- Department of Chemistry, College of Science, University of Agriculture, Faisalabad, Pakistan
| | - Abdullah. G. Al-Sehemi
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
| | - H. Algarni
- Department of Physics, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Javed Iqbal
- Department of Chemistry, College of Science, University of Agriculture, Faisalabad, Pakistan
| | - Mohammad Y. Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
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