1
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Rostamighadi M, Kamelshahroudi A, Pitsitikas V, Jacobson KA, Salavati R. Pilot-Scale Screening of Clinically Approved Drugs to Identify Uridine Insertion/Deletion RNA Editing Inhibitors in Trypanosoma brucei. ACS Infect Dis 2024. [PMID: 39118542 DOI: 10.1021/acsinfecdis.4c00394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
RNA editing pathway is a validated target in kinetoplastid parasites (Trypanosoma brucei, Trypanosoma cruzi, and Leishmania spp.) that cause severe diseases in humans and livestock. An essential large protein complex, the editosome, mediates uridine insertion and deletion in RNA editing through a stepwise process. This study details the discovery of editosome inhibitors by screening a library of widely used human drugs using our previously developed in vitro biochemical Ribozyme Insertion Deletion Editing (RIDE) assay. Subsequent studies on the mode of action of the identified hits and hit expansion efforts unveiled compounds that interfere with RNA-editosome interactions and novel ligase inhibitors with IC50 values in the low micromolar range. Docking studies on the ligase demonstrated similar binding characteristics for ATP and our novel epigallocatechin gallate inhibitor. The inhibitors demonstrated potent trypanocidal activity and are promising candidates for drug repurposing due to their lack of cytotoxic effects. Further studies are necessary to validate these targets using more definitive gene-editing techniques and to enhance the safety profile.
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Affiliation(s)
- Mojtaba Rostamighadi
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3 V9, Canada
| | - Arezou Kamelshahroudi
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3 V9, Canada
| | - Vanessa Pitsitikas
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3 V9, Canada
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, 9000, Rockville Pike, Bethesda, Maryland 20892, United States
| | - Reza Salavati
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3 V9, Canada
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Quebec, Canada
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2
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Rathod S, Dey S, Pawar S, Dhavale R, Choudhari P, Rajakumara E, Mahuli D, Bhagwat D, Tamboli Y, Sankpal P, Mali S, More H. Identification of potential biogenic chalcones against antibiotic resistant efflux pump (AcrB) via computational study. J Biomol Struct Dyn 2024; 42:5178-5196. [PMID: 37340697 DOI: 10.1080/07391102.2023.2225099] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/09/2023] [Indexed: 06/22/2023]
Abstract
The cases of bacterial multidrug resistance are increasing every year and becoming a serious concern for human health. Multidrug efflux pumps are key players in the formation of antibiotic resistance, which transfer out a broad spectrum of drugs from the cell and convey resistance to the host. Efflux pumps have significantly reduced the efficacy of the previously available antibiotic armory, thereby increasing the frequency of therapeutic failures. In gram-negative bacteria, the AcrAB-TolC efflux pump is the principal transporter of the substrate and plays a major role in the formation of antibiotic resistance. In the current work, advanced computer-aided drug discovery approaches were utilized to find hit molecules from the library of biogenic chalcones against the bacterial AcrB efflux pump. The results of the performed computational studies via molecular docking, drug-likeness prediction, pharmacokinetic profiling, pharmacophore mapping, density functional theory, and molecular dynamics simulation study provided ZINC000004695648, ZINC000014762506, ZINC000014762510, ZINC000095099506, and ZINC000085510993 as stable hit molecules against the AcrB efflux pumps. Identified hits could successfully act against AcrB efflux pumps after optimization as lead molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Sreenath Dey
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Swaranjali Pawar
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Rakesh Dhavale
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Eerappa Rajakumara
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Deepak Mahuli
- Department of Pharmacology, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Durgacharan Bhagwat
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Yasinalli Tamboli
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Poournima Sankpal
- Department of Pharmaceutical Chemistry, Ashokrao Mane College of Pharmacy, Kolhapur, MS, India
| | - Sachin Mali
- Department of Pharmaceutics, Y. D. Mane College of Pharmacy, Kagal, MS, India Kolhapur
| | - Harinath More
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
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3
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Tang W, Shen T, Chen Z. In silico discovery of potential PPI inhibitors for anti-lung cancer activity by targeting the CCND1-CDK4 complex via the P21 inhibition mechanism. Front Chem 2024; 12:1404573. [PMID: 38957406 PMCID: PMC11217521 DOI: 10.3389/fchem.2024.1404573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/31/2024] [Indexed: 07/04/2024] Open
Abstract
Non-Small Cell Lung Cancer (NSCLC) is a prevalent and deadly form of lung cancer worldwide with a low 5-year survival rate. Current treatments have limitations, particularly for advanced-stage patients. P21, a protein that inhibits the CCND1-CDK4 complex, plays a crucial role in cell proliferation. Computer-Aided Drug Design (CADD) based on pharmacophores can screen and design PPI inhibitors targeting the CCND1-CDK4 complex. By analyzing known inhibitors, key pharmacophores are identified, and computational methods are used to screen potential PPI inhibitors. Molecular docking, pharmacophore matching, and structure-activity relationship studies optimize the inhibitors. This approach accelerates the discovery of CCND1-CDK4 PPI inhibitors for NSCLC treatment. Molecular dynamics simulations of CCND1-CDK4-P21 and CCND1-CDK4 complexes showed stable behavior, comprehensive sampling, and P21's impact on complex stability and hydrogen bond formation. A pharmacophore model facilitated virtual screening, identifying compounds with favorable binding affinities. Further simulations confirmed the stability and interactions of selected compounds, including 513457. This study demonstrates the potential of CADD in optimizing PPI inhibitors targeting the CCND1-CDK4 complex for NSCLC treatment. Extended simulations and experimental validations are necessary to assess their efficacy and safety.
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Affiliation(s)
| | | | - Zhoumiao Chen
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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4
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Azmal M, Hossen MS, Shohan MNH, Taqui R, Malik A, Ghosh A. A computational approach to identify phytochemicals as potential inhibitor of acetylcholinesterase: Molecular docking, ADME profiling and molecular dynamics simulations. PLoS One 2024; 19:e0304490. [PMID: 38833492 PMCID: PMC11149856 DOI: 10.1371/journal.pone.0304490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/10/2024] [Indexed: 06/06/2024] Open
Abstract
Inhibition of acetylcholinesterase (AChE) is a crucial target in the treatment of Alzheimer's disease (AD). Common anti-acetylcholinesterase drugs such as Galantamine, Rivastigmine, Donepezil, and Tacrine have significant inhibition potential. Due to side effects and safety concerns, we aimed to investigate a wide range of phytochemicals and structural analogues of these compounds. Compounds similar to the established drugs, and phytochemicals were investigated as potential inhibitors for AChE in treating AD. A total of 2,270 compound libraries were generated for further analysis. Initial virtual screening was performed using Pyrx software, resulting in 638 molecules showing higher binding affinities compared to positive controls Tacrine (-9.0 kcal/mol), Donepezil (-7.3 kcal/mol), Galantamine (-8.3 kcal/mol), and Rivastigmine (-6.4 kcal/mol). Subsequently, ADME properties were assessed, including blood-brain barrier permeability and Lipinski's rule of five violations, leading to 88 compounds passing the ADME analysis. Among the rivastigmine analogous, [3-(1-methylpiperidin-2-yl)phenyl] N,N-diethylcarbamate showed interaction with Tyr123, Tyr336, Tyr340, Phe337, Trp285 residues of AChE. Tacrine similar compounds, such as 4-amino-2-styrylquinoline, exhibited bindings with Tyr123, Phe337, Tyr336, Trp285, Trp85, Gly119, and Gly120 residues. A phytocompound (bisdemethoxycurcumin) showed interaction with Trp285, Tyr340, Trp85, Tyr71, and His446 residues of AChE with favourable binding. These findings underscore the potential of these compounds as novel inhibitors of AChE, offering insights into alternative therapeutic avenues for AD. A 100ns simulation analysis confirmed the stability of protein-ligand complex based on the RMSD, RMSF, ligand properties, PCA, DCCM and MMGBS parameters. The investigation suggested 3 ligands as a potent inhibitor of AChE which are [3-(1-methylpiperidin-2-yl)phenyl] N,N-diethylcarbamate, 4-Amino-2-styrylquinoline and bisdemethoxycurcumin. Furthermore, investigation, including in-vitro and in-vivo studies, is needed to validate the efficacy, safety profiles, and therapeutic potential of these compounds for AD treatment.
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Affiliation(s)
- Mahir Azmal
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md. Sahadot Hossen
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md. Naimul Haque Shohan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Rashid Taqui
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Abbeha Malik
- Department of Bioinformatics, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Punjab, Pakistan
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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5
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Berida TI, Adekunle YA, Dada-Adegbola H, Kdimy A, Roy S, Sarker SD. Plant antibacterials: The challenges and opportunities. Heliyon 2024; 10:e31145. [PMID: 38803958 PMCID: PMC11128932 DOI: 10.1016/j.heliyon.2024.e31145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
Nature possesses an inexhaustible reservoir of agents that could serve as alternatives to combat the growing threat of antimicrobial resistance (AMR). While some of the most effective drugs for treating bacterial infections originate from natural sources, they have predominantly been derived from fungal and bacterial species. However, a substantial body of literature is available on the promising antibacterial properties of plant-derived compounds. In this comprehensive review, we address the major challenges associated with the discovery and development of plant-derived antimicrobial compounds, which have acted as obstacles preventing their clinical use. These challenges encompass limited sourcing, the risk of agent rediscovery, suboptimal drug metabolism, and pharmacokinetics (DMPK) properties, as well as a lack of knowledge regarding molecular targets and mechanisms of action, among other pertinent issues. Our review underscores the significance of these challenges and their implications in the quest for the discovery and development of effective plant-derived antimicrobial agents. Through a critical examination of the current state of research, we give valuable insights that will advance our understanding of these classes of compounds, offering potential solutions to the global crisis of AMR. © 2017 Elsevier Inc. All rights reserved.
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Affiliation(s)
- Tomayo I. Berida
- Department of BioMolecular Sciences, Division of Pharmacognosy, University of Mississippi, University, MS, 38677, USA
| | - Yemi A. Adekunle
- Department of Pharmaceutical and Medicinal Chemistry, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, United Kingdom
| | - Hannah Dada-Adegbola
- Department of Medical Microbiology and Parasitology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Ayoub Kdimy
- LS3MN2E, CERNE2D, Faculty of Science, Mohammed V University in Rabat, Rabat, 10056, Morocco
| | - Sudeshna Roy
- Department of BioMolecular Sciences, Division of Pharmacognosy, University of Mississippi, University, MS, 38677, USA
| | - Satyajit D. Sarker
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, United Kingdom
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6
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Lohitha N, Kumar PH, Sarveswari S, Rathod S, Chaudhari S, Tamboli Y, Islam I, Vijayakumar V. Synthesis, Characterization, In Silico DFT, Molecular Docking, and Dynamics Simulation Studies of Phenylhydrazono Phenoxyquinolones for Their Hypoglycemic Efficacy. ACS OMEGA 2024; 9:16384-16399. [PMID: 38617610 PMCID: PMC11007768 DOI: 10.1021/acsomega.4c00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/09/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
A series of novel 24 phenylhydrazono phenoxyquinoline derivatives were synthesized with moderate to excellent yield and screened for their efficacy against the α-amylase enzyme through in silico studies. The structures were characterized using spectroscopic techniques such as 1HNMR, 13CNMR, and HREI-MS. Comprehensive computational studies including, drug-likeness and ADMET profiling, quantum chemical calculations, molecular docking, and molecular dynamics (MD) simulation studies, were performed. A density functional theory study of the synthesized compounds indicated a favorable reactivity profile. The synthesized novel analogues were docked against α-amylase (PDB 6OCN) enzymes to investigate the binding interactions. Based on the docking studies, one of the compounds was found to be the hit with the highest negative binding affinity for α-amylase. A MD simulation study indicated stable binding throughout the simulation.
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Affiliation(s)
- Narayanaswamy Lohitha
- Department
of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Peruru Hemanth Kumar
- Department
of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Sundaramoorthy Sarveswari
- Department
of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Sanket Rathod
- Department
of Pharmaceutical Chemistry, Bharati Vidyapeeth
College of Pharmacy, Kolhapur 416013, Maharashtra, India
| | - Somdatta Chaudhari
- Department
of Pharmaceutical Chemistry, PES’s
Modern College of Pharmacy, Pune 411 044, Maharashtra, India
| | - Yasinalli Tamboli
- King
Abdullah International Medical Research Center (KAIMRC), King Saud
Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh 14811, Saudi Arabia
| | - Imadul Islam
- King
Abdullah International Medical Research Center (KAIMRC), King Saud
Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh 14811, Saudi Arabia
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7
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Meem MH, Yusuf SB, Al Abbad SS, Rahman S, Al-Gawati M, Albrithen H, Alodhayb AN, Uddin KM. Exploring the anticancer and antibacterial potential of naphthoquinone derivatives: a comprehensive computational investigation. Front Chem 2024; 12:1351669. [PMID: 38449478 PMCID: PMC10914998 DOI: 10.3389/fchem.2024.1351669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024] Open
Abstract
This study investigates the potential of 2-(4-butylbenzyl)-3-hydroxynaphthalene-1,4-dione (11) and its 12 derivatives as anticancer and biofilm formation inhibitors for methicillin-resistant staphylococcus aureus using in silico methods. The study employed various computational methods, including molecular dynamics simulation molecular docking, density functional theory, and global chemical descriptors, to evaluate the interactions between the compounds and the target proteins. The docking results revealed that compounds 9, 11, 13, and ofloxacin exhibited binding affinities of -7.6, -7.9, -7.5, and -7.8 kcal mol-1, respectively, against peptide methionine sulfoxide reductase msrA/msrB (PDB: 3E0M). Ligand (11) showed better inhibition for methicillin-resistant staphylococcus aureus msrA/msrB enzyme. The complex of the 3E0M-ligand 11 remained highly stable across all tested temperatures (300, 305, 310, and 320 K). Principal Component Analysis (PCA) was employed to evaluate the behavior of the complex at various temperatures (300, 305, 310, and 320 K), demonstrating a total variance of 85%. Convergence was confirmed by the eigenvector's cosine content value of 0.43, consistently displaying low RMSD values, with the minimum observed at 310 K. Furthermore, ligand 11 emerges as the most promising candidate among the compounds examined, showcasing notable potential when considering a combination of in vitro, in vivo, and now in silico data. While the naphthoquinone derivative (11) remains the primary candidate based on comprehensive in silico studies, further analysis using Frontier molecular orbital (FMO) suggests while the Egap value of compound 11 (2.980 eV) and compound 13 (2.975 eV) is lower than ofloxacin (4.369 eV), indicating their potential, so it can be a statement that compound 13 can also be investigated in further research.
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Affiliation(s)
- Mehnaz Hossain Meem
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Sumaiya Binte Yusuf
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Sanaa S. Al Abbad
- Department of Chemistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Shofiur Rahman
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
| | - Mahmoud Al-Gawati
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hamad Albrithen
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah N. Alodhayb
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Kabir M. Uddin
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
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Rochlani S, Bhatia M, Rathod S, Choudhari P, Dhavale R. Exploration of limonoids for their broad spectrum antiviral potential via DFT, molecular docking and molecular dynamics simulation approach. Nat Prod Res 2024; 38:891-896. [PMID: 37074699 DOI: 10.1080/14786419.2023.2202398] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/07/2023] [Indexed: 04/20/2023]
Abstract
Limonoids serve as vital secondary metabolites. Citrus limonoids show a wide range of pharmacological potential. As a result of which limonoids from citrus are of considerable research interest. Identification of new therapeutic molecules from natural origins has been widely adopted as a successful strategy in drug discovery. This work mainly focused on the high-throughput computational exploration of the antiviral potential of three vital limonoids, i.e. Obacunone, Limonin and Nomilin against spike proteins of SARS CoV-2 (PDB:6LZG), Zika virus NS3 helicase (PDB:5JMT), Serotype 2 RNA dependent RNA polymerase of dengue virus (PDB:5K5M). Herein we report the molecular docking, MD simulation studies of nine docked complexes, and density functional theory (DFT) of selected limonoids. The results of this study indicated that all three limonoids have good molecular features but out of these three obacunone exerted satisfactory results for DFT, docking and MD simulation study.
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Affiliation(s)
- Sneha Rochlani
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Manish Bhatia
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Rakesh Dhavale
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
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9
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Rathod S, Dey S, Choudhari P, Mahuli D, Rochlani S, Dhavale R, Chaudhari S, Tamboli Y, Kilbile J, Rajakumara E. High-throughput computational screening for identification of potential hits against bacterial Acriflavine resistance protein B (AcrB) efflux pump. J Biomol Struct Dyn 2024:1-17. [PMID: 38264919 DOI: 10.1080/07391102.2024.2302936] [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: 11/03/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
Antibiotic resistance is a pressing global health challenge, driven in part by the remarkable efflux capabilities of efflux pump in AcrB (Acriflavine Resistance Protein B) protein in Gram-negative bacteria. In this study, a multi-approached computational screening strategy encompassing molecular docking, In silico absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis, druglikeness assessment, molecular dynamics simulations and density functional theory studies was employed to identify novel hits capable of acting against AcrB-mediated antibiotic resistance. Ligand library was acquired from the COCONUT database. Performed computational analyses unveiled four promising hit molecules (CNP0298667, CNP0399927, CNP0321542 and CNP0269513). Notably, CNP0298667 exhibited the highest negative binding affinity of -11.5 kcal/mol, indicating a possibility of strong potential to disrupt AcrB function. Importantly, all four hits met stringent druglikeness criteria and demonstrated favorable in silico ADMET profiles, underscoring their potential for further development. MD simulations over 100 ns revealed that the CNP0321542-4DX5 and CNP0269513-4DX5 complexes formed robust and stable interactions with the AcrB efflux pump. The identified hits represent a promising starting point for the design and optimization of novel therapeutics aimed at combating AcrB-mediated antibiotic resistance in Gram-negative bacteria.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Sreenath Dey
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology, Hyderabad, Sangareddy, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Deepak Mahuli
- Department of Pharmacology, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Sneha Rochlani
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Rakesh Dhavale
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Somdatta Chaudhari
- Department of Pharmaceutical Chemistry, Progressive Education Society's Modern College of Pharmacy, Nigdi, India
| | - Yasinalli Tamboli
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Jaydeo Kilbile
- University Department of Basic and Applied Sciences (Chemistry), MGM University, Aurangabad, India
| | - Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology, Hyderabad, Sangareddy, India
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10
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Rathod S, Shinde S, Choudhari P, Sarkate A, Chaudhari S, Shingan A. Exploring binding potential of two new indole alkaloids from Nauclea officinalis against third and fourth generation EGFR: druglikeness, in silico ADMET, docking, DFT, molecular dynamics simulation, and MMGBSA study. Nat Prod Res 2024:1-8. [PMID: 38206888 DOI: 10.1080/14786419.2023.2301678] [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: 08/29/2023] [Accepted: 12/29/2023] [Indexed: 01/13/2024]
Abstract
This study investigates the anti-cancer potential of recently discovered indole alkaloids from Nauclea Officinalis against third and fourth-generation EGFR mutations using computational tools. Through ADMET profiling, druglikeness prediction, docking, and simulations, we assessed their pharmacokinetics, binding interactions, and stability. Promising druglikeness and binding affinity were observed, particularly for (±)-19-O-butylangustoline, which demonstrated stronger binding against both EGFR mutants. MD simulations confirmed stable interactions, with (±)-19-O-butylangustoline exhibiting the highest stability. These findings highlight these indole alkaloids as potential anti-cancer agents, with (±)-19-O-butylangustoline warranting further optimisation for therapeutic development. This study informs their potential through insights into molecular properties and binding energetics.
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Affiliation(s)
- Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Sonali Shinde
- Department of Chemical Technology, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Aniket Sarkate
- Department of Chemical Technology, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - Somdatta Chaudhari
- Department of Pharmaceutical Chemistry, Progressive Education Society's Modern College of Pharmacy, Pune, India
| | - Aarti Shingan
- Department of Pharmaceutical Chemistry, Progressive Education Society's Modern College of Pharmacy, Pune, India
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11
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Bakale RD, Sulakhe SM, Kasare SL, Sathe BP, Rathod SS, Choudhari PB, Madhu Rekha E, Sriram D, Haval KP. Design, synthesis and antitubercular assessment of 1, 2, 3-triazole incorporated thiazolylcarboxylate derivatives. Bioorg Med Chem Lett 2024; 97:129551. [PMID: 37979730 DOI: 10.1016/j.bmcl.2023.129551] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/20/2023] [Accepted: 11/09/2023] [Indexed: 11/20/2023]
Abstract
A library of 1, 2, 3-triazole incorporated thiazolylcarboxylate derivatives (7a-q) and (8a-j) were synthesized and evaluated for their in-vitro antitubercular activity against Mycobacterium tuberculosis H37Rv. The two compounds 7h and 8h have displayed excellent antitubercular activity with MIC values of 3.12 and 1.56 µg/mL respectively (MIC values of standard drugs; Ciprofloxacin 1.56 μg/mL & Ethambutol 3.12 μg/mL). Whereas, the four compounds 7i, 7n, 7p and 8i displayed noticeable antitubercular activity with a MIC value of 6.25 µg/mL. The active compounds of the series were further studied for their cytotoxicity against RAW264.7 cell line using MTT assay. Furthermore, to study the probable mechanism of antitubercular action, physicochemical property profiling, DFT calculation and molecular docking study were executed on mycobacterial cell wall target Decaprenylphosphoryl-β-d-ribose 2'-epimerase 1 (DprE1). Among all the compounds, 7h (-10 kcal/mol) and 8h (-10.1 kcal/mol) exerted the highest negative binding affinity against the targeted DprE1 (PDB: 4NCR) protein.
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Affiliation(s)
- Rajubai D Bakale
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University SubCampus, Osmanabad 413501, MS, India
| | - Shubham M Sulakhe
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University SubCampus, Osmanabad 413501, MS, India
| | - Sanghratna L Kasare
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University SubCampus, Osmanabad 413501, MS, India
| | - Bhaurao P Sathe
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University SubCampus, Osmanabad 413501, MS, India
| | - Sanket S Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur 416013, MS, India
| | - Prafulla B Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur 416013, MS, India
| | - Estharla Madhu Rekha
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, R. R. District, Hyderabad 500078, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, R. R. District, Hyderabad 500078, India
| | - Kishan P Haval
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University SubCampus, Osmanabad 413501, MS, India.
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12
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Ogbodo UC, Enejoh OA, Okonkwo CH, Gnanasekar P, Gachanja PW, Osata S, Atanda HC, Iwuchukwu EA, Achilonu I, Awe OI. Computational identification of potential inhibitors targeting cdk1 in colorectal cancer. Front Chem 2023; 11:1264808. [PMID: 38099190 PMCID: PMC10720044 DOI: 10.3389/fchem.2023.1264808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
Introduction: Despite improved treatment options, colorectal cancer (CRC) remains a huge public health concern with a significant impact on affected individuals. Cell cycle dysregulation and overexpression of certain regulators and checkpoint activators are important recurring events in the progression of cancer. Cyclin-dependent kinase 1 (CDK1), a key regulator of the cell cycle component central to the uncontrolled proliferation of malignant cells, has been reportedly implicated in CRC. This study aimed to identify CDK1 inhibitors with potential for clinical drug research in CRC. Methods: Ten thousand (10,000) naturally occurring compounds were evaluated for their inhibitory efficacies against CDK1 through molecular docking studies. The stability of the lead compounds in complex with CDK1 was evaluated using molecular dynamics simulation for one thousand (1,000) nanoseconds. The top-scoring candidates' ADME characteristics and drug-likeness were profiled using SwissADME. Results: Four hit compounds, namely, spiraeoside, robinetin, 6-hydroxyluteolin, and quercetagetin were identified from molecular docking analysis to possess the least binding scores. Molecular dynamics simulation revealed that robinetin and 6-hydroxyluteolin complexes were stable within the binding pocket of the CDK1 protein. Discussion: The findings from this study provide insight into novel candidates with specific inhibitory CDK1 activities that can be further investigated through animal testing, clinical trials, and drug development research for CRC treatment.
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Affiliation(s)
| | - Ojochenemi A. Enejoh
- Genomics and Bioinformatics Department, National Biotechnology Development Agency, Abuja, Nigeria
| | - Chinelo H. Okonkwo
- Department of Pharmacology and Toxicology, University of Nigeria, Nsukka, Nigeria
| | | | - Pauline W. Gachanja
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Shamim Osata
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - Halimat C. Atanda
- Biotechnology Department, Federal University of Technology, Akure, Nigeria
| | - Emmanuel A. Iwuchukwu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, Faculty of Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Ikechukwu Achilonu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, Faculty of Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Olaitan I. Awe
- Department of Computer Science, University of Ibadan, Ibadan, Nigeria
- African Society for Bioinformatics and Computational Biology, Cape Town, South Africa
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13
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Jhinjharia D, Kaushik AC, Sahi S. A high-throughput structural dynamics approach for identification of potential agonists of FFAR4 for type 2 diabetes mellitus therapy. J Biomol Struct Dyn 2023:1-21. [PMID: 37978906 DOI: 10.1080/07391102.2023.2280707] [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: 05/23/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Diabetes mellitus is a metabolic disorder that persists as a global threat to the world. A G-protein coupled receptor (GPCR), free fatty acid receptor 4 (FFAR4), has emerged as a potential target for type 2 diabetes mellitus (T2DM) and obesity-related disorders. The current study has investigated the FFAR4, deploying 3-dimensional structure modeling, molecular docking, machine learning, and high-throughput virtual screening methods to unravel the receptor's crucial and non-crucial binding site residues. We screened four lakh compounds and shortlisted them based on binding energy, stereochemical considerations, non-bonded interactions, and pharmacokinetic profiling. Out of the screened compounds, four compounds were selected for ligand-bound simulations. The molecular dynamic simulations were carried out for 1µs for native FFAR4 and 500 ns each for complexes of FFAR4 with compound 1, compound 2, compound 3, and compound 4. Our findings showed that in addition to reported binding site residues ARG99, ARG183, and VAL98 in known agonists like TUG-891, the amino acids ARG22, ARG24, THR23, TRP305, and GLU43 were also critical binding site residues. These amino acids impart stability to the FFAR4 complexes and contribute to the stronger binding affinity of the compounds. The study also indicated that aromatic residues like PHE211 are crucial for recognizing the active site's pi-pi and C-C double bonds. Since FFAR4 is a membrane protein, the simulation studies give an insight into the mechanisms of the crucial protein-lipid and lipid-water interactions. The analysis of the molecular dynamics trajectories showed all four compounds as potential hit molecules that can be developed further into potential agonists for T2DM therapy. Amongst the four compounds, compound 4 showed relatively better binding affinity, stronger non-bonded interactions, and a stable complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Divya Jhinjharia
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Aman Chandra Kaushik
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shakti Sahi
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
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14
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Borah SM, Kma L, Darjee MS, Deka D, Lyngdoh A, Sharan RN, Baruah TJ. Apigenin promotes cell death in NCI-H23 cells by upregulation of PTEN: potential involvement of the binding of apigenin with WWP2 protein. J Biomol Struct Dyn 2023:1-15. [PMID: 37870050 DOI: 10.1080/07391102.2023.2272743] [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: 04/11/2023] [Accepted: 08/21/2023] [Indexed: 10/24/2023]
Abstract
The tumour suppressor protein PTEN is often down-regulated in non-small cell lung cancer. A major protein promoting the lowering of the PTEN protein is WWP2. Polyphenols have been shown to promote the expression of tumour suppressor genes like PTEN. We carry out the study to check for the ability of apigenin to bind with the WWP2 protein using in-silico investigation comprising docking and simulation. We checked for the cytotoxic effect of apigenin upon the non-small cell lung cancer cell line NCI-H23. We checked the PTEN expression status at the gene and protein levels. The expression levels of the apoptotic regulators BCL2, BAX and CASPASE3 genes along with the activity levels of the caspase-3 protein were checked. The ultrastructure of the cells was analysed. Our Autodock analysis showed that apigenin bound favourably with the WWP2 protein. Molecular dynamics simulation revealed that apigenin increased the parameters of RMSD, Rg and SASA when bound with the WWP2 protein. The protein-ligand complex had hydrogen bonding and majorly van der Wal's interactions. PCA analysis revealed greater fluctuations in the apigenin-bound state of the protein. The mutant form of the WWP2 revealed similar results in the presence of apigenin. Apigenin showed efficacy against the NCI-H23 cell line and promoted PTEN protein levels, lowered BCL2 gene expression and up-regulated BAX and CASPASE3 gene expression. Increased caspase-3 activity and ultra-structural analysis revealed the occurrence of apoptosis. Thus the binding of apigenin with WWP2 could promote PTEN protein levels and lead to apoptotic activity in NCI-H23 cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sapna Mayuri Borah
- Department of Plant Pathology, Assam Agricultural University, Jorhat, India
| | - Lakhon Kma
- Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | | | - Dikshit Deka
- Department of Biochemistry, Assam Royal Global University, Guwahati, India
| | - Anisha Lyngdoh
- Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Rajesh N Sharan
- Department of Biochemistry, Assam Royal Global University, Guwahati, India
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15
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Choudhari S, Patil SK, Rathod S. Identification of hits as anti-obesity agents against human pancreatic lipase via docking, drug-likeness, in-silico ADME(T), pharmacophore, DFT, molecular dynamics, and MM/PB(GB)SA analysis. J Biomol Struct Dyn 2023:1-23. [PMID: 37735906 DOI: 10.1080/07391102.2023.2258407] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
Obesity, characterized by excessive fat accumulation, is a major health concern. Inhibition of human pancreatic lipase, an enzyme involved in fat digestion, offers a potential strategy for weight loss and obesity treatment. This study aimed to identify polyphenols capable of forming stable complexes with human pancreatic lipase to block its activity. Molecular docking, density functional theory (DFT), molecular dynamics (MD) simulations, and MMPBGBSA calculations were employed to evaluate ligand binding, stability, and energy profiles. Pharmacophore modeling was also performed to identify key structural features for effective inhibition. Virtual screening identified ZINC000015120539, ZINC000000899200, ZINC000001531702, and ZINC000013340267 as potential candidates, exhibiting favorable binding and stable interactions over 100 ns MD simulations. These findings provide insights into the inhibitory potential of selected polyphenols on human pancreatic lipase and support further experimental investigations for obesity treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sujata Choudhari
- Department of Pharmaceutical Chemistry, Sarojini College of Pharmacy, Kolhapur, MS, India
- Department of Pharmaceutics, Ashokrao Mane College of Pharmacy, Peth Vadgaon, MS, India
| | - Sachin Kumar Patil
- Department of Pharmaceutics, Ashokrao Mane College of Pharmacy, Peth Vadgaon, MS, India
| | - Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
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16
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Rathod S, Chavan P, Mahuli D, Rochlani S, Shinde S, Pawar S, Choudhari P, Dhavale R, Mudalkar P, Tamboli F. Exploring biogenic chalcones as DprE1 inhibitors for antitubercular activity via in silico approach. J Mol Model 2023; 29:113. [PMID: 36971900 DOI: 10.1007/s00894-023-05521-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/17/2023] [Indexed: 03/28/2023]
Abstract
Cases of drug-resistant tuberculosis (TB) have increased worldwide in the last few years, and it is a major threat to global TB control strategies and the human population. Mycobacterium tuberculosis is a common causative agent responsible for increasing cases of TB and as reported by WHO, approximately, 1.5 million death occurred from TB in 2020. Identification of new therapies against drug-resistant TB is an urgent need to be considered primarily. The current investigation aims to find the potential biogenic chalcone against the potential targets of drug-resistant TB via in silico approach. The ligand library of biogenic chalcones was screened against DprE1. Results of molecular docking and in silico ADMET prediction revealed that ZINC000005158606 has lead-like properties against the targeted protein. Pharmacophore modeling was done to identify the pharmacophoric features and their geometric distance present in ZINC000005158606. The binding stability study performed using molecular dynamics (MD) simulation of the DprE1-ZINC000005158606 complex revealed the conformational stability of the complex system over 100 ns with minimum deviation. Further, the in silico anti-TB sensitivity of ZINC000005158606 was found to be higher as compared to the standards against Mycobacterium tuberculosis. The overall in silico investigation indicated the potential of identified hit to act as a lead molecule against Mycobacterium tuberculosis.
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