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Ibrahim PEGF, Zuccotto F, Zachariae U, Gilbert I, Bodkin M. Accurate prediction of dynamic protein-ligand binding using P-score ranking. J Comput Chem 2024; 45:1762-1778. [PMID: 38647338 DOI: 10.1002/jcc.27370] [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: 10/20/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/25/2024]
Abstract
Protein-ligand binding prediction typically relies on docking methodologies and associated scoring functions to propose the binding mode of a ligand in a biological target. Significant challenges are associated with this approach, including the flexibility of the protein-ligand system, solvent-mediated interactions, and associated entropy changes. In addition, scoring functions are only weakly accurate due to the short time required for calculating enthalpic and entropic binding interactions. The workflow described here attempts to address these limitations by combining supervised molecular dynamics with dynamical averaging quantum mechanics fragment molecular orbital. This combination significantly increased the ability to predict the experimental binding structure of protein-ligand complexes independent from the starting position of the ligands or the binding site conformation. We found that the predictive power could be enhanced by combining the residence time and interaction energies as descriptors in a novel scoring function named the P-score. This is illustrated using six different protein-ligand targets as case studies.
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Affiliation(s)
- Peter E G F Ibrahim
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Fabio Zuccotto
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Ulrich Zachariae
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Ian Gilbert
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Mike Bodkin
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
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2
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Eyush E, Kumar S, Sen K, Sakarwal A, Ram H, Yadav D, Kumar A, Panwar A. Protective efficacy of nafronyl in diabetic retinopathy through targeted inhibition of key enzymes. Biotechnol Appl Biochem 2024. [PMID: 38898746 DOI: 10.1002/bab.2625] [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: 11/28/2023] [Accepted: 05/27/2024] [Indexed: 06/21/2024]
Abstract
Diabetic retinopathy is governed by abnormal apoptosis, increased capillary pressure, and other linked pathology that needs an efficient treatment by multitargeted approaches. Thus, the current study aimed to explore the potential of inhibition of targeted enzymes (DPP4, ACE-2, and aldose reductase) and free radical scavenging capabilities of selected compounds (nafronyl or naftidrofuryl) through in silico and in vivo investigations. Significant binding energies were observed in complexes of aldolase reductase, angiotensin type 1 receptor, and DPP4 against the nafronyl and sitagliptin more than -7.5 kcal/mol. Further validation of free energy was confirmed by calculations of molecular mechanics Poisson-Boltzmann surface area (MMPBSA), and configurational stabilities examined by PCA (principal component analysis). Additionally, drug-likeness was examined by the Swiss ADME web tool, which showed significant findings. Consequently, in vivo experimentations showed significant inflammation and alterations in retinal layers of inner plexiform (inner limiting membrane, nerve fibers, and ganglionic cells), inner nuclear layer (bipolar cells and horizontal cells), and photoreceptors cells. Whereas the treatments (nafronyl and sitagliptin) caused significant improvements in the histoarchitecture of the retina. Additionally, the HOMA indices (IR-insulin resistance, sensitivity, and β cells functioning) and levels of free radicals were significantly altered in the diabetic control group in comparison to intact control. Nafronyl administration showed significant ameliorations in HOMA indices as well as antioxidant levels. Based on the results, it can be concluded that nafronyl efficiently interacts with target enzymes, which may result in potent inhibition and ameliorations in retinal histology as well as glucose homeostasis and antioxidants.
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Affiliation(s)
- Eyush Eyush
- Department of Biochemistry, Central University of Haryana, Mahendragrah, India
| | - Shivani Kumar
- School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Karishma Sen
- Department of Zoology, Jai Narain Vyas University, Jodhpur, India
| | - Anita Sakarwal
- Department of Zoology, Jai Narain Vyas University, Jodhpur, India
| | - Heera Ram
- Department of Zoology, Jai Narain Vyas University, Jodhpur, India
| | - Dharamveer Yadav
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, India
| | - Antresh Kumar
- Department of Biochemistry, Central University of Haryana, Mahendragrah, India
| | - Anil Panwar
- Department of Bioinformatics and Computational Biology, CCS Haryana Agricultural University, Hisar, India
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3
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Krivoshchapov NV, Medvedev MG. Accurate and Efficient Conformer Sampling of Cyclic Drug-Like Molecules with Inverse Kinematics. J Chem Inf Model 2024; 64:4542-4552. [PMID: 38776465 DOI: 10.1021/acs.jcim.3c02040] [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: 05/25/2024]
Abstract
Identification of all of the influential conformers of biomolecules is a crucial step in many tasks of computational biochemistry. Specifically, molecular docking, a key component of in silico drug development, requires a comprehensive set of conformations for potential candidates in order to generate the optimal ligand-receptor poses and, ultimately, find the best drug candidates. However, the presence of flexible cycles in a molecule complicates the initial search for conformers since exhaustive sampling algorithms via torsional random and systematic searches become very inefficient. The devised inverse-kinematics-based Monte Carlo with refinement (MCR) algorithm identifies independently rotatable dihedral angles in (poly)cyclic molecules and uses them to perform global conformational sampling, outperforming popular alternatives (MacroModel, CREST, and RDKit) in terms of speed and diversity of the resulting conformer ensembles. Moreover, MCR quickly and accurately recovers naturally occurring macrocycle conformations for most of the considered molecules.
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Affiliation(s)
- Nikolai V Krivoshchapov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Michael G Medvedev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
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4
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Abdjan MI, Shafiq M, Nerukh D, Nur-E-Alam M, Ul-Haq Z. Exploring the mechanism of action of spirooxindoles as a class of CDK2 inhibitors: a structure-based computational approach. Phys Chem Chem Phys 2024; 26:16139-16152. [PMID: 38787638 DOI: 10.1039/d4cp00844h] [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: 05/26/2024]
Abstract
Cyclin-dependent kinase 2 (CDK2) regulates cell cycle checkpoints in the synthesis and mitosis phases and plays a pivotal role in cancerous cell proliferation. The activation of CDK2, influenced by various protein signaling pathways, initiates the phosphorylation process. Due to its crucial role in carcinogenesis, CDK2 is a druggable hotspot target to suppress cancer cell proliferation. In this context, several studies have identified spirooxindoles as an effective class of CDK2 inhibitors. In the present study, three spirooxindoles (SOI1, SOI2, and SOI3) were studied to understand their inhibitory mechanism against CDK2 through a structure-based approach. Molecular docking and molecular dynamics (MD) simulations were performed to explore their interactions with CDK2 at the molecular level. The calculated binding free energy for the spirooxindole-based CDK2 inhibitors aligned well with experimental results regarding CDK2 inhibition. Energy decomposition (ED) analysis identified key binding residues, including I10, G11, T14, R36, F82, K89, L134, P155, T158, Y159, and T160, in the CDK2 active site and T-loop phosphorylation. Molecular mechanics (MM) energy was identified as the primary contributor to stabilizing inhibitor binding in the CDK2 protein structure. Furthermore, the analysis of binding affinity revealed that the inhibitor SOI1 binds more strongly to CDK2 compared to the other inhibitors under investigation. It demonstrated a robust interaction with the crucial residue T160 in the T-loop phosphorylation site, responsible for kinase activation. These insights into the inhibitory mechanism are anticipated to contribute to the development of potential CDK2 inhibitors using the spirooxindole scaffold.
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Affiliation(s)
- Muhammad Ikhlas Abdjan
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C UNAIR, Jl. Mulyorejo, Surabaya, Indonesia
| | - Muhammad Shafiq
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Dmitry Nerukh
- Department of Mathematics, Aston University, Birmingham, B4 7ET, UK
| | - Mohammad Nur-E-Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box. 2457, Riyadh 11451, Kingdom of Saudi Arabia.
| | - Zaheer Ul-Haq
- Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
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5
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Tian T, Li S, Zhang Z, Chen L, Zou Z, Zhao D, Zeng J. Benchmarking compound activity prediction for real-world drug discovery applications. Commun Chem 2024; 7:127. [PMID: 38834746 DOI: 10.1038/s42004-024-01204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
Identifying active compounds for target proteins is fundamental in early drug discovery. Recently, data-driven computational methods have demonstrated promising potential in predicting compound activities. However, there lacks a well-designed benchmark to comprehensively evaluate these methods from a practical perspective. To fill this gap, we propose a Compound Activity benchmark for Real-world Applications (CARA). Through carefully distinguishing assay types, designing train-test splitting schemes and selecting evaluation metrics, CARA can consider the biased distribution of current real-world compound activity data and avoid overestimation of model performances. We observed that although current models can make successful predictions for certain proportions of assays, their performances varied across different assays. In addition, evaluation of several few-shot training strategies demonstrated different performances related to task types. Overall, we provide a high-quality dataset for developing and evaluating compound activity prediction models, and the analyses in this work may inspire better applications of data-driven models in drug discovery.
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Affiliation(s)
- Tingzhong Tian
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Shuya Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Ziting Zhang
- Department of Automation, Tsinghua University, Beijing, China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Lin Chen
- Silexon AI Technology Co., Ltd., Nanjing, Jiangsu Province, China
| | - Ziheng Zou
- Silexon AI Technology Co., Ltd., Nanjing, Jiangsu Province, China
| | - Dan Zhao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China.
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China.
- School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China.
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6
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Zhou S, Zhang H, Li J, Li W, Su M, Ren Y, Ge F, Zhang H, Shang H. Potential anti-liver cancer targets and mechanisms of kaempferitrin based on network pharmacology, molecular docking and experimental verification. Comput Biol Med 2024; 178:108693. [PMID: 38850960 DOI: 10.1016/j.compbiomed.2024.108693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/29/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
AIM Kaempferitrin is an active component in Chenopodium ambrosioides, showing medicinal functions against liver cancer. This study aimed to identify the potential targets and pathways of kaempferitrin against liver cancer using network pharmacology and molecular docking, and verify the essential hub targets and pathway in mice model of SMMC-7721 cells xenografted tumors and SMMC-7721 cells. METHODS Kaempferitrin therapeutical targets were obtained by searching SwissTargetPrediction, PharmMapper, STITCH, DrugBank, and TTD databases. Liver cancer specific genes were obtained by searching GeneCards, DrugBank, TTD, OMIM, and DisGeNET databases. PPI network of "kaempferitrin-targets-liver cancer" was constructed to screen the hub targets. GO, KEGG pathway and MCODE clustering analyses were performed to identify possible enrichment of genes with specific biological subjects. Molecular docking and molecular dynamics simulation were employed to determine the docking pose, potential and stability of kaempferitrin with hub targets. The potential anti-liver cancer mechanisms of kaempferitrin, as predicted by network pharmacology analyses, were verified by in vitro and in vivo experiments. RESULTS 228 kaempferitrin targets and 2186 liver cancer specific targets were identified, of which 50 targets were overlapped. 8 hub targets were identified through network topology analysis, and only SIRT1 and TP53 had a potent binding activity with kaempferitrin as indicated by molecular docking and molecular dynamics simulation. MCODE clustering analysis revealed the most significant functional module of PPI network including SIRT1 and TP53 was mainly related to cell apoptosis. GO and KEGG enrichment analyses suggested that kaempferitrin exerted therapeutic effects on liver cancer possibly by promoting apoptosis via p21/Bcl-2/Caspase 3 signaling pathway, which were confirmed by in vivo and in vitro experiments, such as HE staining of tumor tissues, CCK-8, qRT-PCR and Western blot. CONCLUSION This study provided not only insight into how kaempferitrin could act against liver cancer by identifying hub targets and their associated signaling pathways, but also experimental evidence for the clinical use of kaempferitrin in liver cancer treatment.
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Affiliation(s)
- Siyu Zhou
- College of Life Science, Sichuan Normal University, Chengdu, 610101, China
| | - Huidong Zhang
- College of Life Science, Sichuan Normal University, Chengdu, 610101, China
| | - Jiao Li
- College of Life Science, Sichuan Normal University, Chengdu, 610101, China.
| | - Wei Li
- College of Life Science, Sichuan Normal University, Chengdu, 610101, China
| | - Min Su
- College of Life Science, Sichuan Normal University, Chengdu, 610101, China
| | - Yao Ren
- College of Life Science, Sichuan Normal University, Chengdu, 610101, China
| | - Fanglan Ge
- College of Life Science, Sichuan Normal University, Chengdu, 610101, China
| | - Hong Zhang
- College of Life Science, Sichuan Normal University, Chengdu, 610101, China
| | - Hongli Shang
- College of Life Science, Sichuan Normal University, Chengdu, 610101, China
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7
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Herlah B, Janežič M, Ogris I, Grdadolnik SG, Kološa K, Žabkar S, Žegura B, Perdih A. Nature-inspired substituted 3-(imidazol-2-yl) morpholines targeting human topoisomerase IIα: Dynophore-derived discovery. Biomed Pharmacother 2024; 175:116676. [PMID: 38772152 DOI: 10.1016/j.biopha.2024.116676] [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: 03/12/2024] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 05/23/2024] Open
Abstract
The molecular nanomachine, human DNA topoisomerase IIα, plays a crucial role in replication, transcription, and recombination by catalyzing topological changes in the DNA, rendering it an optimal target for cancer chemotherapy. Current clinical topoisomerase II poisons often cause secondary tumors as side effects due to the accumulation of double-strand breaks in the DNA, spurring the development of catalytic inhibitors. Here, we used a dynamic pharmacophore approach to develop catalytic inhibitors targeting the ATP binding site of human DNA topoisomerase IIα. Our screening of a library of nature-inspired compounds led to the discovery of a class of 3-(imidazol-2-yl) morpholines as potent catalytic inhibitors that bind to the ATPase domain. Further experimental and computational studies identified hit compound 17, which exhibited selectivity against the human DNA topoisomerase IIα versus human protein kinases, cytotoxicity against several human cancer cells, and did not induce DNA double-strand breaks, making it distinct from clinical topoisomerase II poisons. This study integrates an innovative natural product-inspired chemistry and successful implementation of a molecular design strategy that incorporates a dynamic component of ligand-target molecular recognition, with comprehensive experimental characterization leading to hit compounds with potential impact on the development of more efficient chemotherapies.
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Affiliation(s)
- Barbara Herlah
- National Institute of Chemistry, Hajdrihova 19, Ljubljana SI 1000, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana SI 1000, Slovenia
| | - Matej Janežič
- National Institute of Chemistry, Hajdrihova 19, Ljubljana SI 1000, Slovenia
| | - Iza Ogris
- National Institute of Chemistry, Hajdrihova 19, Ljubljana SI 1000, Slovenia; University of Ljubljana, Faculty of Medicine, Vrazov trg 2, Ljubljana SI 1000, Slovenia
| | | | - Katja Kološa
- National institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 121, Ljubljana SI 1000, Slovenia
| | - Sonja Žabkar
- National institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 121, Ljubljana SI 1000, Slovenia
| | - Bojana Žegura
- National institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 121, Ljubljana SI 1000, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, Ljubljana SI 1000, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana SI 1000, Slovenia.
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8
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Patel D, Sethi N, Patel P, Shah S, Patel K. Exploring the potential of P-glycoprotein inhibitors in the targeted delivery of anti-cancer drugs: A comprehensive review. Eur J Pharm Biopharm 2024; 198:114267. [PMID: 38514020 DOI: 10.1016/j.ejpb.2024.114267] [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: 11/24/2023] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
Due to the high prevalence of cancer, progress in the management of cancer is the need of the hour. Most cancer patients develop chemotherapeutic drug resistance, and many remain insidious due to overexpression of Multidrug Resistance Protein 1 (MDR1), also known as Permeability-glycoprotein (P-gp) or ABCB1 transporter (ATP-binding cassette subfamily B member 1). P-gp, a transmembrane protein that protects vital organs from outside chemicals, expels medications from malignant cells. The blood-brain barrier (BBB), gastrointestinal tract (GIT), kidneys, liver, pancreas, and cancer cells overexpress P-gp on their apical surfaces, making treatment inefficient and resistant. Compounds that compete with anticancer medicines for transportation or directly inhibit P-gp may overcome biological barriers. Developing nanotechnology-based formulations may help overcome P-gp-mediated efflux and improve bioavailability and cell chemotherapeutic agent accumulation. Nanocarriers transport pharmaceuticals via receptor-mediated endocytosis, unlike passive diffusion, which bypasses ABCB1. Anticancer drugs and P-gp inhibitors in nanocarriers may synergistically increase drug accumulation and chemotherapeutic agent toxicity. The projection of desirable binding and effect may be procured initially by molecular docking of the inhibitor with P-gp, enabling the reduction of preliminary trials in formulation development. Here, P-gp-mediated efflux and several possible outcomes to overcome the problems associated with currently prevalent cancer treatments are highlighted.
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Affiliation(s)
- Dhvani Patel
- Department of Pharmaceutical Technology, L. J. Institute of Pharmacy, L J University, Ahmedabad 382 210, India
| | - Nutan Sethi
- Department of Pharmaceutical Technology, L. J. Institute of Pharmacy, L J University, Ahmedabad 382 210, India
| | - Paresh Patel
- Department of Pharmaceutical Chemistry, L. J. Institute of Pharmacy, L J University, Ahmedabad 382 210, India
| | - Shreeraj Shah
- Department of Pharmaceutical Technology, L. J. Institute of Pharmacy, L J University, Ahmedabad 382 210, India
| | - Kaushika Patel
- Department of Pharmaceutical Technology, L. J. Institute of Pharmacy, L J University, Ahmedabad 382 210, India.
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9
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Moi D, Vittorio S, Angeli A, Supuran CT, Onnis V. Discovery of a New Class of 1-(4-Sulfamoylbenzoyl)piperidine-4-carboxamides as Human Carbonic Anhydrase Inhibitors. ACS Med Chem Lett 2024; 15:470-477. [PMID: 38628786 PMCID: PMC11017293 DOI: 10.1021/acsmedchemlett.3c00484] [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: 11/09/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 04/19/2024] Open
Abstract
A series of 1-(4-sulfamoylbenzoyl)piperidine-4-carboxamides deriving from substituted piperazines/benzylamines was designed, synthesized, and tested on human carbonic anhydrase (hCA). The inhibitory activity of the new sulfonamides was analyzed using acetazolamide (AAZ) as a standard inhibitor against hCA I, II, IX, and XII. Several sulfonamides showed both inhibitory activity at low nanomolar concentrations and selectivity against the cytosolic hCA II isoform, and the same trend was observed on the tumor-associated hCA IX and XII. The benzenesulfonamido carboxamides 11 and 15 were the most potent of the piperazino- and benzylamino-based series, respectively. Docking and molecular dynamics studies related the high selectivity of compound 11 toward the tumor-associated hCA isoforms to its capability to participate in favorable interactions within hCA IX and hCA XII active sites, whereas no such interactions were detected within both hCA I and hCA II isoforms.
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Affiliation(s)
- Davide Moi
- Dipartimento
di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, 09042 Cagliari, Italy
| | - Serena Vittorio
- Dipartimento
di Scienze Farmaceutiche, Università
degli Studi di Milano, 20122 Milano, Italy
| | - Andrea Angeli
- Laboratorio
di Chimica Bioinorganica, Polo Scientifico Neurofarba Department, Università Degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
| | - Claudiu T. Supuran
- Laboratorio
di Chimica Bioinorganica, Polo Scientifico Neurofarba Department, Università Degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
| | - Valentina Onnis
- Dipartimento
di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, 09042 Cagliari, Italy
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10
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Venanzi NE, Basciu A, Vargiu AV, Kiparissides A, Dalby PA, Dikicioglu D. Machine Learning Integrating Protein Structure, Sequence, and Dynamics to Predict the Enzyme Activity of Bovine Enterokinase Variants. J Chem Inf Model 2024; 64:2681-2694. [PMID: 38386417 PMCID: PMC11005043 DOI: 10.1021/acs.jcim.3c00999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
Despite recent advances in computational protein science, the dynamic behavior of proteins, which directly governs their biological activity, cannot be gleaned from sequence information alone. To overcome this challenge, we propose a framework that integrates the peptide sequence, protein structure, and protein dynamics descriptors into machine learning algorithms to enhance their predictive capabilities and achieve improved prediction of the protein variant function. The resulting machine learning pipeline integrates traditional sequence and structure information with molecular dynamics simulation data to predict the effects of multiple point mutations on the fold improvement of the activity of bovine enterokinase variants. This study highlights how the combination of structural and dynamic data can provide predictive insights into protein functionality and address protein engineering challenges in industrial contexts.
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Affiliation(s)
| | - Andrea Basciu
- Department
of Physics, University of Cagliari, Cittadella
Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Attilio Vittorio Vargiu
- Department
of Physics, University of Cagliari, Cittadella
Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Alexandros Kiparissides
- Department
of Biochemical Engineering, University College
London, Gower Street, WC1E 6BT London, U.K.
- Department
of Chemical Engineering, Aristotle University
of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Paul A. Dalby
- Department
of Biochemical Engineering, University College
London, Gower Street, WC1E 6BT London, U.K.
| | - Duygu Dikicioglu
- Department
of Biochemical Engineering, University College
London, Gower Street, WC1E 6BT London, U.K.
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11
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Chatterjee P, Karn R, Emerson IA, Banerjee S. Docking and Molecular Dynamics Simulation Revealed the Potential Inhibitory Activity of Amygdalin in Triple-Negative Breast Cancer Therapeutics Targeting the BRCT Domain of BARD1 Receptor. Mol Biotechnol 2024; 66:718-736. [PMID: 36732462 DOI: 10.1007/s12033-023-00680-8] [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: 08/31/2022] [Accepted: 01/23/2023] [Indexed: 02/04/2023]
Abstract
Triple-negative breast cancer (TNBC), is diagnosed as the most lethal molecular subtype of breast cancer (BC) preceded by an extremely poor prognosis. For enabling effective TNBC therapy, the identification of novel druggable biomarkers is an earnest need. Multigene paneling and genomewide association studies identify multiple genes with high-to-moderate penetrance in TNBC. Modern computer-aided drug designing techniques, thus aim to design more cost-effective natural small molecule inhibitors for TNBC prevention and diagnosis. Here Amygdalin, a natural glycosidic inhibitor is docked and simulated against three such high-to-moderate penetrance genes identified in TNBC, BARD1, RAD51, and PALB2. The preliminary result of the analysis, reports a highest, intermediate, and least binding energy score of - 6.69 kcal/mol, - 5.09 kcal/mol, and - 4.89 kcal/mol in BARD1, RAD51, and PALB2, respectively. The best-docked protein-ligand complex (BARD1-Amygdalin) was then simulated and compared with an approved drug for TNBC treatment, Olaparib. A comparable binding energy score of - 8.53 kcal/mol was obtained by docking olaparib with BARD1. A 100 ns MD simulation revealed, Amygdalin forms more H-bonds, providing more stable and compact protein-ligand complex with BARD1 than compared to Olaparib. The result was also supported by calculation of solvent accessible surface area and analysis of radius of gyration. Thus, our findings suggest that role of Amygdalin can further be studied in details for TNBC therapeutics, which was found to target the BRCT domain of the BARD1 receptor in stable manner. Please check and confirm that the authors and their respective affiliations have been correctly identified and amend if necessary. Name and affiliations are correctly identified.
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Affiliation(s)
- Prarthana Chatterjee
- School of BioSciences and Technology, Vellore Institute of Technology, 632014, Vellore, Tamil Nadu, India
| | - Rohit Karn
- School of BioSciences and Technology, Vellore Institute of Technology, 632014, Vellore, Tamil Nadu, India
| | - I Arnold Emerson
- School of BioSciences and Technology, Vellore Institute of Technology, 632014, Vellore, Tamil Nadu, India
| | - Satarupa Banerjee
- School of BioSciences and Technology, Vellore Institute of Technology, 632014, Vellore, Tamil Nadu, India.
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12
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Fernández-Ochoa Á, Younis IY, Arafa RK, Cádiz-Gurrea MDLL, Leyva-Jiménez FJ, Segura Carretero A, Mohsen E, Saber FR. Metabolite Profiling of Colvillea racemosa via UPLC-ESI-QTOF-MS Analysis in Correlation to the In Vitro Antioxidant and Cytotoxic Potential against A549 Non-Small Cell Lung Cancer Cell Line. PLANTS (BASEL, SWITZERLAND) 2024; 13:976. [PMID: 38611505 PMCID: PMC11013431 DOI: 10.3390/plants13070976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
In this study, flower and leaf extracts of Colvillea racemosa were considered a source of bioactive compounds. In this context, the objective of the study focused on investigating the anticancer potential as well as the phytochemical composition of both extracts. The extracts were analyzed by UPLC-ESI-QTOF-MS, and the bioactivity was tested using in vitro antioxidant assays (FRAP, DPPH, and ABTS) in addition to cytotoxic assays on non-small cell lung cancer cell line (A549). Our results clearly indicated the potent radical scavenging capacity of both extracts. Importantly, the flower extract exhibited a greater antioxidant capacity than the leaf extract. In terms of cytotoxic activity, leaf and flower extracts significantly inhibited cell viability with IC50 values of 17.0 and 17.2 µg/mL, respectively. The phytochemical characterization enabled the putative annotation of 42 metabolites, such as saccharides, phenolic acids, flavonoids, amino acids, and fatty acids. Among them, the flavonoid C-glycosides stand out due to their high relative abundance and previous reports on their anticancer bioactivity. For a better understanding of the bioactive mechanisms, four flavonoids (vitexin, kaempferol-3-O-rutinoside, luteolin, and isoorientin) were selected for molecular docking on hallmark protein targets in lung cancer as represented by γ-PI3K, EGFR, and CDK2 through in-silico studies. In these models, kaempferol-3-O-rutinoside and vitexin had the highest binding scores on γ-PI3K and CDK2, followed by isoorientin, so they could be highly responsible for the bioactive properties of C. racemosa extracts.
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Affiliation(s)
- Álvaro Fernández-Ochoa
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Avda Fuentenueva s/n, 18071 Granada, Spain; (M.d.l.L.C.-G.); (F.J.L.-J.); (A.S.C.)
| | - Inas Y. Younis
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Kasr el-Aini Street, Cairo 11562, Egypt; (I.Y.Y.); (E.M.)
| | - Reem K. Arafa
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Cairo 12578, Egypt;
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo 12578, Egypt
| | - María de la Luz Cádiz-Gurrea
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Avda Fuentenueva s/n, 18071 Granada, Spain; (M.d.l.L.C.-G.); (F.J.L.-J.); (A.S.C.)
| | - Francisco Javier Leyva-Jiménez
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Avda Fuentenueva s/n, 18071 Granada, Spain; (M.d.l.L.C.-G.); (F.J.L.-J.); (A.S.C.)
- Department of Analytical Chemistry and Food Science and Technology, University of Castilla-La Mancha, Ronda de Calatrava, 7, 13071 Ciudad Real, Spain
| | - Antonio Segura Carretero
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Avda Fuentenueva s/n, 18071 Granada, Spain; (M.d.l.L.C.-G.); (F.J.L.-J.); (A.S.C.)
| | - Engy Mohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Kasr el-Aini Street, Cairo 11562, Egypt; (I.Y.Y.); (E.M.)
| | - Fatema R. Saber
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Kasr el-Aini Street, Cairo 11562, Egypt; (I.Y.Y.); (E.M.)
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13
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Naderi A, Akıncıoğlu A, Çağan A, Çelikkaleli H, Akıncıoğlu H, Göksu S. Design, synthesis and anticholinergic properties of novel α-benzyl dopamine, tyramine, and phenethylamine derivatives. Bioorg Chem 2024; 144:107146. [PMID: 38262088 DOI: 10.1016/j.bioorg.2024.107146] [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: 10/13/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Abstract
Due to the important biological properties of dopamine, phenethylamine, and tyramine derivatives in the central nervous system, herein the synthesis of novel α-benzyl dopamine, phenethylamine, and tyramine derivatives is described. The title compounds were synthesized starting from 3-phenylpropanoic acids and methoxybenzenes in six or seven steps. Firstly, 3-(2,3-dimethoxyphenyl)propanoic acid (11) and 3-(3,4-dimethoxyphenyl)propanoic acid (12) were selectively brominated with N-bromosuccinimide (NBS). The Friedel-Crafts acylation of methoxylated benzenes with these brominated acids or commercially available 3-phenylpropanoic acid in polyphosphoric acid gave the desired dihydrochalcones. α-Carboxylation of dihydrochalcones, reduction of benzylic carbonyl groups, hydrolysis of esters to acid derivatives, and the Curtius rearrangement reaction of acids followed by in situ synthesis of carbamates from alkyl isocyanates and hydrogenolysis of the carbamates afforded the title compounds in good total yields. Alzheimer's disease (AD) and Parkinson's disease (PD) are chronic neurodegenerative diseases that become serious over time. However, the exact pathophysiology of both diseases has not been revealed yet. There have been many different approaches to the treatment of patients for many years, especially studies on the cholinergic system cover a wide area. Within the scope of this study, the inhibition effects of dopamine-derived carbamates and amine salts on the cholinergic enzymes AChE and BChE were examined. Dopamine-derived carbamate 24a-i showed inhibition in the micro-nanomolar range; compound 24d showed a Ki value of 26.79 nM against AChE and 3.33 nM against BChE, while another molecule, 24i, showed a Ki range of 27.24 nM and 0.92 nM against AChE and BChE, respectively. AChE and BChE were effectively inhibited by dopamine-derived amine salts 25j-s, with Ki values in the range of 17.70 to 468.57 µM and 0.76-211.23 µM, respectively. Additionally, 24c, 24e and 25m were determined to be 60, 276 and 90 times more selective against BChE than AChE, respectively.
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Affiliation(s)
- Ali Naderi
- Atatürk University, Faculty of Science, Department of Chemistry, Erzurum, Turkiye
| | - Akın Akıncıoğlu
- Ağrı İbrahim Çeçen University, Central Researching Laboratory, 04100, Ağrı, Turkiye; Vocational School, Ağrı İbrahim Çeçen University, 04100, Ağrı, Turkiye
| | - Ahmet Çağan
- Ağrı İbrahim Çeçen University, Central Researching Laboratory, 04100, Ağrı, Turkiye
| | - Hilal Çelikkaleli
- Atatürk University, Faculty of Science, Department of Chemistry, Erzurum, Turkiye
| | - Hülya Akıncıoğlu
- Ağrı İbrahim Çeçen University, Faculty of Arts and Science, 04100 Ağrı, Turkiye
| | - Süleyman Göksu
- Atatürk University, Faculty of Science, Department of Chemistry, Erzurum, Turkiye.
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14
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Kausar MA, Rabie AM, Azam F, Anwar S, Alenazi F, Alshammari KF, Kar S, Ali A, AboElnaga SMH, Jamal A, Singh G, Thakur L, Najm MZ, Saeed M. The role of Aedes aegypti in inducing/aggravating IgE-mediated allergic airway disease: extensive computational studies for identification of allergenic proteins. J Biomol Struct Dyn 2024; 42:2738-2745. [PMID: 37194307 DOI: 10.1080/07391102.2023.2212305] [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: 02/07/2023] [Accepted: 04/19/2023] [Indexed: 05/18/2023]
Abstract
Respiratory allergies have become a major public health concern and affect one-third of the world's population. Several factors like environmental changes, industrialization, and immunologic interactions are reported to contribute to allergic respiratory diseases. Immunological reactions because of mosquito bite (allergic proteins) have been reported to have a high contribution to IgE-mediated allergic airway disease but they are largely ignored. In this study, we aim to predict the potential allergens (proteins) from Aedes aegypti that might play a role in the reactions of IgE-mediated allergic airway diseases. The allergens are identified from an extensive literature search and the 3D structures were prepared using the SwissDock server. Computational studies were performed to identify the potential allergens that might be responsible for IgE-mediated allergies. Our docking and molecular dynamics (MD) simulation results suggest that ADE-3, an allergen from Aedes aegypti, has the highest docking score and is predicted to be responsible for IgE-mediated allergic reaction(s). Overall, this study highlights the importance of immunoinformatics, and the obtained information can be used for designing prophylactic peptide vaccine candidates and inhibitors for controlling IgE-mediated inflammations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohd A Kausar
- Department of Biochemistry, College of Medicine, University of Ha'il, Ha'il, Saudi Arabia
| | - Amgad M Rabie
- Head of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Dikernis, Dakahlia Governorate, Egypt
| | - Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Saudi Arabia
| | - Sadaf Anwar
- Department of Biochemistry, College of Medicine, University of Ha'il, Ha'il, Saudi Arabia
| | - Fahaad Alenazi
- Department of Pharmacology, College of Medicine, University of Ha'il, Ha'il, Saudi Arabia
| | - Khalid F Alshammari
- Department of Internal Medicine, College of Medicine, University of Ha'il, Ha'il, Saudi Arabia
| | - Subhabrata Kar
- School of Biosciences, Apeejay Stya University, Gurugram, India
| | - Abrar Ali
- Department of Ophthalmology, College of Medicine, University of Ha'il, Ha'il, Saudi Arabia
| | - Shimaa M H AboElnaga
- Department of Basic Science, Deanship of Preparatory Year, University of Ha'il, Ha'il, Saudi Arabia
| | - Azfar Jamal
- Health and Basic Science Research Centre, Majmaah University, Majmaah, Riyadh Region, Saudi Arabia
- Department of Biology, College of Science, Al-Zulfi, Majmaah University, Majmaah, Riyadh Region, Saudi Arabia
| | - Gagandeep Singh
- Section of Microbiology, Central Ayurveda Research Institute, Jhansi, Uttar Pradesh, India
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi, India
| | - Lovnish Thakur
- School of Biosciences, Apeejay Stya University, Gurugram, India
| | - Mohammad Z Najm
- School of Biosciences, Apeejay Stya University, Gurugram, India
| | - Mohd Saeed
- Department of Biology, College of Sciences, University of Ha'il, Ha'il, Saudi Arabia
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15
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Kumar S, Bhowmik R, Oh JM, Abdelgawad MA, Ghoneim MM, Al-Serwi RH, Kim H, Mathew B. Machine learning driven web-based app platform for the discovery of monoamine oxidase B inhibitors. Sci Rep 2024; 14:4868. [PMID: 38418571 PMCID: PMC10901862 DOI: 10.1038/s41598-024-55628-y] [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: 01/04/2024] [Accepted: 02/26/2024] [Indexed: 03/01/2024] Open
Abstract
Monoamine oxidases (MAOs), specifically MAO-A and MAO-B, play important roles in the breakdown of monoamine neurotransmitters. Therefore, MAO inhibitors are crucial for treating various neurodegenerative disorders, including Parkinson's disease (PD), Alzheimer's disease (AD), and amyotrophic lateral sclerosis (ALS). In this study, we developed a novel cheminformatics pipeline by generating three diverse molecular feature-based machine learning-assisted quantitative structural activity relationship (ML-QSAR) models concerning MAO-B inhibition. PubChem fingerprints, substructure fingerprints, and one-dimensional (1D) and two-dimensional (2D) molecular descriptors were implemented to unravel the structural insights responsible for decoding the origin of MAO-B inhibition in 249 non-reductant molecules. Based on a random forest ML algorithm, the final PubChem fingerprint, substructure fingerprint, and 1D and 2D molecular descriptor prediction models demonstrated significant robustness, with correlation coefficients of 0.9863, 0.9796, and 0.9852, respectively. The significant features of each predictive model responsible for MAO-B inhibition were extracted using a comprehensive variance importance plot (VIP) and correlation matrix analysis. The final predictive models were further developed as a web application, MAO-B-pred ( https://mao-b-pred.streamlit.app/ ), to allow users to predict the bioactivity of molecules against MAO-B. Molecular docking and dynamics studies were conducted to gain insight into the atomic-level molecular interactions between the ligand-receptor complexes. These findings were compared with the structural features obtained from the ML-QSAR models, which supported the mechanistic understanding of the binding phenomena. The presented models have the potential to serve as tools for identifying crucial molecular characteristics for the rational design of MAO-B target inhibitors, which may be used to develop effective drugs for neurodegenerative disorders.
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Affiliation(s)
- Sunil Kumar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, India
| | - Ratul Bhowmik
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Jong Min Oh
- Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Mohamed A Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, 72341, Sakaka, Aljouf, Saudi Arabia
| | - Mohammed M Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, 13713, Ad Diriyah, Riyadh, Saudi Arabia
| | - Rasha Hamed Al-Serwi
- Department of Basic Dental Sciences, College of Dentistry, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, 11671, Riyadh, Saudi Arabia
| | - Hoon Kim
- Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922, Republic of Korea.
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, India.
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16
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Tyukina SP, Velmiskina JA, Dmitrienko AO, Medvedev MG. Binomial Uncertainty in Molecular Dynamics-Based Reactions Analysis. J Phys Chem Lett 2024; 15:2105-2110. [PMID: 38358803 DOI: 10.1021/acs.jpclett.3c03540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Molecular Dynamics-based reaction analysis is an indispensable tool for studying processes defying the transition-state theory (TST), where the product ratios do not follow energies of transition states. The main class of such processes is ambimodal reactions, which have a post-transition-state bifurcation, so that several products form via a single transition state. Multiple runs of molecular dynamics allow one to sample the space of possibilities and ultimately predict the product ratio without relying on TST; however, no techniques for estimating the reliability of the prediction were proposed so far. Here we show that dynamics runs follow the same rules as die rolls, which paves a simple way for estimating their uncertainty and, accordingly, the number of runs necessary to achieve the required accuracy. Remarkably, we find that the majority of such studies carried out in the last 5 years use far too few runs, so that the product ratios predicted in them can be off by >50% in more than 50% of cases.
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Affiliation(s)
- Sofya P Tyukina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow, Russian Federation
- National Research University Higher School of Economics, Myasnitskaya Street 20, 101000 Moscow, Russian Federation
| | - Julia A Velmiskina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow, Russian Federation
| | - Artem O Dmitrienko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow, Russian Federation
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russian Federation
| | - Michael G Medvedev
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow, Russian Federation
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17
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Amen Y, Selim MA, Suef RA, Sayed AM, Othman A. Unveiling the Antiviral Efficacy of Forskolin: A Multifaceted In Vitro and In Silico Approach. Molecules 2024; 29:704. [PMID: 38338448 PMCID: PMC10856047 DOI: 10.3390/molecules29030704] [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: 01/02/2024] [Revised: 01/27/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Coleus forskohlii (Willd.) Briq. is a medicinal herb of the Lamiaceae family. It is native to India and widely present in the tropical and sub-tropical regions of Egypt, China, Ethiopia, and Pakistan. The roots of C. forskohlii are edible, rich with pharmaceutically bioactive compounds, and traditionally reported to treat a variety of diseases, including inflammation, respiratory disorders, obesity, and viral ailments. Notably, the emergence of viral diseases is expected to quickly spread; consequently, these data impose a need for various approaches to develop broad active therapeutics for utilization in the management of future viral infectious outbreaks. In this study, the naturally occurring labdane diterpenoid derivative, Forskolin, was obtained from Coleus forskohlii. Additionally, we evaluated the antiviral potential of Forskolin towards three viruses, namely the herpes simplex viruses 1 and 2 (HSV-1 and HSV-2), hepatitis A virus (HAV), and coxsackievirus B4 (COX-B4). We observed that Forskolin displayed antiviral activity against HAV, COX-B4, HSV-1, and HSV-2 with IC50 values of 62.9, 73.1, 99.0, and 106.0 μg/mL, respectively. Furthermore, we explored the Forskolin's potential antiviral target using PharmMapper, a pharmacophore-based virtual screening platform. Forskolin's modeled structure was analyzed to identify potential protein targets linked to its antiviral activity, with results ranked based on Fit scores. Cathepsin L (PDB ID: 3BC3) emerged as a top-scoring hit, prompting further exploration through molecular docking and MD simulations. Our analysis revealed that Forskolin's binding mode within Cathepsin L's active site, characterized by stable hydrogen bonding and hydrophobic interactions, mirrors that of a co-crystallized inhibitor. These findings, supported by consistent RMSD profiles and similar binding free energies, suggest Forskolin's potential in inhibiting Cathepsin L, highlighting its promise as an antiviral agent.
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Affiliation(s)
- Yhiya Amen
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed A Selim
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo 11884, Egypt; (M.A.S.); (R.A.S.)
| | - Reda A. Suef
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo 11884, Egypt; (M.A.S.); (R.A.S.)
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Collage of Pharmacy, Almaaqal University, Basrah 61014, Iraq;
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt
| | - Ahmed Othman
- Department of Pharmacognosy and Medicinal Plants, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
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18
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Azevedo PHRDA, Peçanha BRDB, Flores-Junior LAP, Alves TF, Dias LRS, Muri EMF, Lima CHDS. In silico drug repurposing by combining machine learning classification model and molecular dynamics to identify a potential OGT inhibitor. J Biomol Struct Dyn 2024; 42:1417-1428. [PMID: 37054524 DOI: 10.1080/07391102.2023.2199868] [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: 10/20/2022] [Accepted: 04/01/2023] [Indexed: 04/15/2023]
Abstract
O-linked N-acetylglucosamine (O-GlcNAc) is a unique intracellular post-translational glycosylation at the hydroxyl group of serine or threonine residues in nuclear, cytoplasmic and mitochondrial proteins. The enzyme O-GlcNAc transferase (OGT) is responsible for adding GlcNAc, and anomalies in this process can lead to the development of diseases associated with metabolic imbalance, such as diabetes and cancer. Repurposing approved drugs can be an attractive tool to discover new targets reducing time and costs in the drug design. This work focuses on drug repurposing to OGT targets by virtual screening of FDA-approved drugs through consensus machine learning (ML) models from an imbalanced dataset. We developed a classification model using docking scores and ligand descriptors. The SMOTE approach to resampling the dataset showed excellent statistical values in five of the seven ML algorithms to create models from the training set, with sensitivity, specificity and accuracy over 90% and Matthew's correlation coefficient greater than 0.8. The pose analysis obtained by molecular docking showed only H-bond interaction with the OGT C-Cat domain. The molecular dynamics simulation showed the lack of H-bond interactions with the C- and N-catalytic domains allowed the drug to exit the binding site. Our results showed that the non-steroidal anti-inflammatory celecoxib could be a potentially OGT inhibitor.
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Affiliation(s)
| | | | | | - Tatiana Fialho Alves
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Luiza Rosaria Sousa Dias
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Estela Maris Freitas Muri
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, Brazil
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19
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Xie J, Zhang X, Meng D, Li Y, Deng P. Identification of potentially high drug-like VEGFR2/c-Met dual-target type II kinase inhibitors with symmetric skeletons based on structural screening. J Biomol Struct Dyn 2024; 42:1249-1267. [PMID: 37042992 DOI: 10.1080/07391102.2023.2199082] [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: 12/23/2022] [Accepted: 03/29/2023] [Indexed: 04/13/2023]
Abstract
Vascular endothelial growth factor receptor 2 (VEGFR2) and c-Mesenchymal epithelial transition factor (c-Met) are tyrosine kinase receptors associated with the occurrence of malignant tumors. Studies have shown that inhibition of VEGFR2 promotes a feedback increase in c-Met, a mechanism linked to the emergence of resistance to VEGFR2 inhibitors. Therefore, treatment targeting both VEGFR2 and c-Met will have better application prospects. In this study, hierarchical virtual screening was performed on ZINC15, Molport and Mcule-ULTIMATE databases to identify potential VEGFR2/c-Met dual inhibitors. Firstly, the best pharmacophore model for each target was used to cross-screen the three databases, and the compounds that could match the two pharmacophore models were then retained based on the Fit Value of the respective crystal ligands. Compounds ZINC, MOL, and MLB named after their database sources were retained by binding pattern analysis and docking assessment. ADMET predictions indicated that ZINC had significantly higher oral bioavailability compared to the approved drug cabozantinib. This is likely due to ZINC's unique symmetrical backbone with less structure complexity, which may reduce the occurrence of adverse effects. Molecular dynamics simulations and binding free energy analysis showed that all three hit compounds were able to stably bind at the active site, but only ZINC could form high occupancy of hydrogen bonds with both VEGFR2 and c-Met, and also only ZINC had a higher binding free energy than crystal ligands, suggesting that ZINC was the most likely potential VEGFR2/c-Met dual-target inhibitor. This finding provides a promising starting point for the development of VEGFR2/c-Met dual-target inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiali Xie
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, China
- Chongqing Key Research Laboratory for Quality Evaluation and Safety Research of APIs, Chongqing, China
| | - Xiaoxuan Zhang
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, China
- Chongqing Key Research Laboratory for Quality Evaluation and Safety Research of APIs, Chongqing, China
| | - Dan Meng
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, China
- Chongqing Key Research Laboratory for Quality Evaluation and Safety Research of APIs, Chongqing, China
| | - Yihao Li
- College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Ping Deng
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, China
- Chongqing Key Research Laboratory for Quality Evaluation and Safety Research of APIs, Chongqing, China
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20
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Kim SM, Kang SH, Jeon BW, Kim YH. Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration. BIORESOURCE TECHNOLOGY 2024; 394:130248. [PMID: 38158090 DOI: 10.1016/j.biortech.2023.130248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.
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Affiliation(s)
- Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Sung Heuck Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea; Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
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21
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Vincenzi M, Mercurio FA, Leone M. Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools. Int J Mol Sci 2024; 25:1798. [PMID: 38339078 PMCID: PMC10855943 DOI: 10.3390/ijms25031798] [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: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).
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Affiliation(s)
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy; (M.V.); (F.A.M.)
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Alamfard T, Lorenz T, Breitkopf C. Glass Transition Temperatures and Thermal Conductivities of Polybutadiene Crosslinked with Randomly Distributed Sulfur Chains Using Molecular Dynamic Simulation. Polymers (Basel) 2024; 16:384. [PMID: 38337272 DOI: 10.3390/polym16030384] [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: 12/24/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
The thermal conductivities and glass transition temperatures of polybutadiene crosslinked with randomly distributed sulfur chains having different lengths from mono-sulfur (S1) to octa-sulfur (S8) were investigated. The thermal conductivities of the related models as a function of the heat flux autocorrelation function, applying an equilibrium molecular dynamic (EMD) simulation and the Green-Kubo method, were studied for a wide range of temperatures. The influence of the length of sulfur chains, degree of crosslinking, and molar mass of the crosslinker on the glass transition temperature and final values of thermal conductivities were studied. First, the degree of crosslinking is considered constant for the eight simulation models, from mono-sulfur (S1) to octa-sulfur (S8), while the molar mass of the sulfur is increases. The results show that the thermal conductivities of the crosslinked structure decrease with increasing temperature for each model. Moreover, by increasing the lengths of the sulfur chains and the molar weight of the crosslinker, thermal conductivity increases at a constant temperature. The MD simulation demonstrates that the glass transition temperature and density of the crosslinked structure enhance as the length of the sulfur chains and molar mass of the sulfur increase. Second, the molar weight of sulfur is considered constant in these eight models; therefore, the degree of crosslinking decreases with the increase in the lengths of the sulfur chains. The results show that the thermal conductivities of the crosslinked structure decrease with the increase in the temperature for each model. Moreover, by increasing the lengths of sulfur chains and thus decreasing the degree of crosslinking, the trend in changes in thermal conductivities are almost the same for all of these models, so thermal conductivity is constant for a specific temperature. In addition, the glass transition temperature and density of the crosslinked structure decrease.
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Affiliation(s)
- Tannaz Alamfard
- Chair of Thermodynamics, Institute of Power Engineering, Faculty of Mechanical Engineering, Technical University Dresden, 01069 Dresden, Germany
| | - Tommy Lorenz
- Chair of Thermodynamics, Institute of Power Engineering, Faculty of Mechanical Engineering, Technical University Dresden, 01069 Dresden, Germany
| | - Cornelia Breitkopf
- Chair of Thermodynamics, Institute of Power Engineering, Faculty of Mechanical Engineering, Technical University Dresden, 01069 Dresden, Germany
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Peluso P, Chankvetadze B. Recent developments in molecular modeling tools and applications related to pharmaceutical and biomedical research. J Pharm Biomed Anal 2024; 238:115836. [PMID: 37939549 DOI: 10.1016/j.jpba.2023.115836] [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: 08/05/2023] [Revised: 09/21/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
In modern pharmaceutical and biomedical research, molecular modeling represents a useful tool to explore processes and their mechanistic bases at the molecular level. Integrating experimental and virtual analysis is a fruitful approach to study ligand-receptor interaction in chemical, biochemical and biological environments. In these fields, molecular docking and molecular dynamics are considered privileged techniques for modeling (bio)macromolecules and related complexes. This review aims to present the current landscape of molecular modeling in pharmaceutical and biomedical research by examining selected representative applications published in the last years and highlighting current topics and trends of this field. Thus, a systematic compilation of all published literature has not been attempted herein. After a brief overview of the main theoretical and computational tools used to investigate mechanisms at molecular level, recent applications of molecular modeling in drug discovery, ligand binding and for studying protein conformation and function will be discussed. Furthermore, specific sections will be devoted to the application of molecular modeling for unravelling enantioselective mechanisms underlying the enantioseparation of chiral compounds of pharmaceutical and biomedical interest as well as for studying new forms of noncovalent interactivity identified in biochemical and biological environments. The general aim of this review is to provide the reader with a modern overview of the topic, highlighting advancements and outlooks as well as drawbacks and pitfalls still affecting the applicability of theoretical and computational methods in the field of pharmaceutical and biomedical research.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB-CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy.
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, 0179 Tbilisi, Georgia
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24
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Mkabayi L, Viljoen Z, Krause RW, Lobb KA, Pletschke BI, Frost CL. Inhibitory effects of selected cannabinoids against dipeptidyl peptidase IV, an enzyme linked to type 2 diabetes. Heliyon 2024; 10:e23289. [PMID: 38169946 PMCID: PMC10758829 DOI: 10.1016/j.heliyon.2023.e23289] [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: 09/16/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Ethnopharmacological relevance In recent times the decriminalisation of cannabis globally has increased its use as an alternative medication. Where it has been used in modern medicinal practises since the 1800s, there is limited scientific investigation to understand the biological activities of this plant. Aim of the study Dipeptidyl peptidase IV (DPP-IV) plays a key role in regulating glucose homeostasis, and inhibition of this enzyme has been used as a therapeutic approach to treat type 2 diabetes. However, some of the synthetic inhibitors for this enzyme available on the market may cause undesirable side effects. Therefore, it is important to identify new inhibitors of DPP-IV and to understand their interaction with this enzyme. Methods In this study, four cannabinoids (cannabidiol, cannabigerol, cannabinol and Δ9-tetrahydrocannabinol) were evaluated for their inhibitory effects against recombinant human DPP-IV and their potential inhibition mechanism was explored using both in vitro and in silico approaches. Results All four cannabinoids resulted in a dose-dependent response with IC50 values of between 4.0 and 6.9 μg/mL. Kinetic analysis revealed a mixed mode of inhibition. CD spectra indicated that binding of cannabinoids results in structural and conformational changes in the secondary structure of the enzyme. These findings were supported by molecular docking studies which revealed best docking scores at both active and allosteric sites for all tested inhibitors. Furthermore, molecular dynamics simulations showed that cannabinoids formed a stable complex with DPP-IV protein via hydrogen bonds at an allosteric site, suggesting that cannabinoids act by either inducing conformational changes or blocking the active site of the enzyme. Conclusion These results demonstrated that cannabinoids may modulate DPP-IV activity and thereby potentially assist in improving glycaemic regulation in type 2 diabetes.
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Affiliation(s)
- Lithalethu Mkabayi
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, 6140, South Africa
| | - Zenobia Viljoen
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | - Rui W.M. Krause
- Department of Chemistry, Rhodes University, Makhanda, 6140, South Africa
| | - Kevin A. Lobb
- Department of Chemistry, Rhodes University, Makhanda, 6140, South Africa
| | - Brett I. Pletschke
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, 6140, South Africa
| | - Carminita L. Frost
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, 6031, South Africa
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Jiang SL, Wang WJ, Hu ZY, Zhang RJ, Shi JH. Comprehending the intermolecular interaction of JAK inhibitor fedratinib with bovine serum albumin (BSA)/human alpha-1-acid glycoprotein (HAG): Multispectral methodologies and molecular simulation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123277. [PMID: 37625199 DOI: 10.1016/j.saa.2023.123277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/31/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
The primary coverage of this paper is to investigate the molecular interaction of JAK2 inhibitor, fedratinib (FED) with BSA/HAG proteins through multispectral approaches and molecular docking as well as MD calculation. Arrival at a conclusion, the endogenous fluorescence of BSA/HAG protein was quenched separately in the form of static and mixed quenching. The FED-BSA and FED-HAG complexes with the stoichiometric ratio of 1:1 were formed in the interaction process. And, The Kb values of these complexes were of 104-105 M-1 and 105-106 M-1, respectively, representing that the FED-HAG complex exhibited a comparatively high affinity compared to the FED-BSA complex. It is confimed that FED inserted into the interface area between subdomain IIA and IIB of BSA (marked as site II') and the bucket-shaped hydrophobic cavity of HAG, respectively, resulting in the slight alteration in the secondary structure of BSA/HAG and the micro-environment round Tyr and Trp residues. The expetimental results also confirmed that van der Waals forces (VDW), hydrogen bonds and hydrophobic interaction played a dominant role in the formation of two stable complexes. The above experimental results were supplemented and verified through molecular docking and MD simulation. Meanwhile, the effects of common ions on affinity were explored. This study could shine a light on evaluating the pharmacological properties of the JAK inhibitor FED, understanding the distribution and operation of the drug in the body, and leading to the development of the creation of novel medication devise.
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Affiliation(s)
- Shao-Liang Jiang
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou 310032, China.
| | - Wan-Jun Wang
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhe-Ying Hu
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Rong-Juan Zhang
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Jie-Hua Shi
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou 310032, China.
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Alotaibi MO, Alotaibi NM, Alwaili MA, Alshammari N, Adnan M, Patel M. Natural sapogenins as potential inhibitors of aquaporins for targeted cancer therapy: computational insights into binding and inhibition mechanism. J Biomol Struct Dyn 2024:1-22. [PMID: 38174738 DOI: 10.1080/07391102.2023.2299743] [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: 09/02/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Aquaporins (AQPs) are membrane proteins that facilitate the transport of water and other small molecules across biological membranes. AQPs are involved in various physiological processes and pathological conditions, including cancer, making them as potential targets for anticancer therapy. However, the development of selective and effective inhibitors of AQPs remains a challenge. In this study, we explored the possibility of using natural sapogenins, a class of plant-derived aglycones of saponins with diverse biological activities, as potential inhibitors of AQPs. We performed molecular docking, dynamics simulation and binding energy calculation to investigate the binding and inhibition mechanism of 19 sapogenins against 13 AQPs (AQP0-AQP13) that are overexpressed in various cancers. Our results showed that out of 19 sapogenins, 8 (Diosgenin, Gitogenin, Tigogenin, Ruscogenin, Yamogenin, Hecogenin, Sarsasapogenin and Smilagenin) exhibited acceptable drug-like characteristics. These sapogenin also exhibited favourable binding affinities in the range of -7.6 to -13.4 kcal/mol, and interactions within the AQP binding sites. Furthermore, MD simulations provided insights into stability and dynamics of the sapogenin-AQP complexes. Most of the fluctuations in binding pocket were observed for AQP0-Gitogenin and AQP4-Diosgenin. However, remaining protein-ligand complex showed stable root mean square deviation (RMSD) plots, strong hydrogen bonding interactions, stable solvent-accessible surface area (SASA) values and minimum distance to the receptor. These observations suggest that natural sapogenin hold promise as novel inhibitors of AQPs, offering a basis for the development of innovative therapeutic agents for cancer treatment. However, further validation of the identified compounds through experiments is essential for translating these findings into therapeutic applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Modhi O Alotaibi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nahaa M Alotaibi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Maha Abdullah Alwaili
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mitesh Patel
- Research and Development Cell, Department of Biotechnology, Parul Institute of Applied Sciences, Parul University, Vadodara, India
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Chen YM, Lu CT, Wang CW, Fischer WB. Repurposing dye ligands as antivirals via a docking approach on viral membrane and globular proteins - SARS-CoV-2 and HPV-16. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184220. [PMID: 37657640 DOI: 10.1016/j.bbamem.2023.184220] [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: 07/24/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
A series of dye ligands are docked to three different proteins, E and 3a of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) and E6 of human papilloma virus type 16 (HPV-16) using three different software. A four-level selection algorithm is used based on nonparametric statistics of numerical key values such as the "rank" derived from (i) averaged estimated binding energies (EBEs) and (ii) absolute EBE value of each of the software, (iii) frequency of ranking and (iv) rank of the area-under-curve values (AUCs) from decoy docking. A series of repurposing drugs and known antivirals used in experimental studies are docked for comparison. One dye ligand is ranked best for all proteins using the selection algorithm levels i - iii. Another three dye ligands are ranked top for the proteins individually when using all four levels.
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Affiliation(s)
- Yi-Ming Chen
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ching-Tai Lu
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chia-Wen Wang
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wolfgang B Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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Jiang SL, Li L, Kou SB, Hu L, Shi JH. Insight into intermolecular binding mechanism of apatinib mesylate and human alpha-1-acid glycoprotein: combined multi-spectroscopic approaches with in silico. J Biomol Struct Dyn 2024; 42:779-790. [PMID: 37000929 DOI: 10.1080/07391102.2023.2195015] [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: 01/18/2023] [Accepted: 03/19/2023] [Indexed: 04/03/2023]
Abstract
Apatinib mesylate (APM), an oral tyrosine kinase inhibitor, has a good anti-tumor activity in the treatment of various cancers, particularly in advanced non-small cell lung cancer. In this study, the intermolecular binding mechanism between APM and human alpha-1-acid glycoprotein (HAG) was investigated by combining multi-spectroscopic approaches with in silico techniques. The findings revealed that APM gave rise to the fluorescence quenching of HAG by forming a ground-state complex between APM and HAG with a stoichiometric ratio of 1:1, and APM has a moderate affinity for HAG as the binding constant of APM and HAG of approximately 105 M-1, which was larger than the APM-HAG complex. The findings from thermodynamic parameter analysis indicated that the dominant driving forces for the formation of the APM-HAG complex were van der Waals forces, hydrogen bonding and hydrophobic interactions, which were also verified with site-probe studies and molecular docking. The findings from in silico study indicated that APM inserted into the opening of the hydrophobic cavity of HAG, leads to a slight conformational change in the HAG, which was verified by circular dichroism (CD) measurements, that was, the beta sheet level of HAG decreased. Additionally, the results of synchronous and 3D fluorescence spectroscopies confirmed the decline in hydrophobicity of the microenvironment around Trp and Tyr residues. Moreover, some common metal ions such as Cu2+, Mg2+, Fe3+, Ca2+, and Zn2+ could cause the alteration in the binding constant of APM with HAG, leading to the change in the efficacy of APM. It will be expected that these study findings are to provide useful information for further understanding pharmacokinetic and structural modifications of APM.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shao-Liang Jiang
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou, China
| | - Li Li
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou, China
| | - Song-Bo Kou
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou, China
| | - Lu Hu
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou, China
| | - Jie-Hua Shi
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou, China
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29
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Dos Santos JC, Alves JEF, de Azevedo RDS, de Lima ML, de Oliveira Silva MR, da Silva JG, da Silva JM, de Carvalho Correia AC, do Carmo Alves de Lima M, de Oliveira JF, de Moura RO, de Almeida SMV. Study of nitrogen heterocycles as DNA/HSA binder, topoisomerase inhibitors and toxicological safety. Int J Biol Macromol 2024; 254:127651. [PMID: 37949265 DOI: 10.1016/j.ijbiomac.2023.127651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Four new nitrogen-containing heterocyclic derivatives (acridine, quinoline, indole, pyridine) were synthesized and their biological properties were evaluated. The compounds showed affinity for DNA and HSA, with CAIC and CAAC displaying higher binding constants (Kb) of 9.54 × 104 and 1.06 × 106, respectively. The fluorescence quenching assay (Ksv) revealed suppression values ranging from 0.34 to 0.64 × 103 M-1 for ethidium bromide (EB) and 0.1 to 0.34 × 103 M-1 for acridine orange (AO). Molecular docking confirmed the competition of the derivatives with intercalation probes at the same binding site. At 10 μM concentrations, the derivatives inhibited topoisomerase IIα activity. In the antiproliferative assays, the compounds demonstrated activity against MCF-7 and T47-D tumor cells and nonhemolytic profile. Regarding toxicity, no acute effects were observed in the embryos. However, some compounds caused enzymatic and cardiac changes, particularly the CAIC, which increased SOD activity and altered heart rate compared to the control. These findings suggest potential antitumor action of the derivatives and indicate that substituting the acridine core with different cores does not interfere with their interaction and topoisomerase inhibition. Further investigations are required to assess possible toxicological effects, including reactive oxygen species generation.
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Affiliation(s)
- Jéssica Celerino Dos Santos
- Molecular Biology Laboratory, University of Pernambuco (UPE), Multicampi Garanhuns, Garanhuns, PE 55290-000, Brazil
| | | | | | - Maksuelly Libanio de Lima
- Molecular Biology Laboratory, University of Pernambuco (UPE), Multicampi Garanhuns, Garanhuns, PE 55290-000, Brazil
| | | | - Josefa Gerlane da Silva
- Molecular Biology Laboratory, University of Pernambuco (UPE), Multicampi Garanhuns, Garanhuns, PE 55290-000, Brazil
| | - Jamire Muriel da Silva
- Department of Pharmacy, Laboratory of Synthesis and Vectorization of Molecules, State University of Paraíba (UEPB), Campus Campina Grande, 58429-500, PB, Brazil
| | | | - Maria do Carmo Alves de Lima
- Chemistry and Therapeutic Innovation Laboratory (LQIT), Department of Antibiotics, Federal University of Pernambuco, Recife, PE, Brazil
| | | | - Ricardo Olímpio de Moura
- Department of Pharmacy, Laboratory of Synthesis and Vectorization of Molecules, State University of Paraíba (UEPB), Campus Campina Grande, 58429-500, PB, Brazil
| | - Sinara Mônica Vitalino de Almeida
- Molecular Biology Laboratory, University of Pernambuco (UPE), Multicampi Garanhuns, Garanhuns, PE 55290-000, Brazil; Keizo Asami Immunopathology Laboratory (LIKA), Federal University of Pernambuco, Recife, PE, Brazil; Chemistry and Therapeutic Innovation Laboratory (LQIT), Department of Antibiotics, Federal University of Pernambuco, Recife, PE, Brazil.
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30
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Zhang Y, Zhang D, Li M, Qin Q, Jin Y, Fang Y, Sun G. Molecular docking and dynamics of a dextranase derived from Penicillium cyclopium CICC-4022. Int J Biol Macromol 2023; 253:126493. [PMID: 37648125 DOI: 10.1016/j.ijbiomac.2023.126493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/04/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
This study aimed to investigate the recognition mechanism of dextranase (PC-Edex) produced by Penicillium cyclopium CICC-4022 on dextran. Whole genome information of P. cyclopium CICC-4022 was obtained through genome sequencing technology. The coding information of PC-Edex was determined based on the annotation of the protein-coding genes using protein databases. The three-dimensional structure of PC-Edex was obtained via homology modelling. The active site and binding free energy between PC-Edex and dextran were calculated by molecular docking and molecular dynamics techniques. The results showed that the total sequence length and GC content of P. cyclopium CICC-4022 were 29,710,801 bp and 47.02 %, respectively. The annotation of protein-encoding genes showed that P. cyclopium CICC-4022 is highly active and has many carbohydrate transport and metabolic functions, and most of its proteases are glycolytic anhydrases. Furthermore, the gene encoding PC-Edex was successfully annotated. Molecular dynamics simulations indicated that van der Waals interaction was the main driving force of interaction. Residues Ile114, Asp115, Tyr332, Lys344, and Gln403 significantly promoted the binding between dextran and PC-Edex. In summary, this study explored the active site catalyzed by PC-Edex based on the binding pattern of PC-Edex and dextran. Therefore, this study provides genomic information on dextranase and data supporting the rational modification and enhancement of PC-Edex.
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Affiliation(s)
- Yirui Zhang
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China
| | - Donghui Zhang
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China
| | - Mei Li
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China; Key Laboratory of Chemical and Biological Transforming Process of Guangxi Higher Education Institutes, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China.
| | - Qin Qin
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China; Key Laboratory of Chemical and Biological Transforming Process of Guangxi Higher Education Institutes, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China
| | - Yuhui Jin
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China
| | - Yan Fang
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China
| | - Guoliang Sun
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China
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Shimu MSS, Paul GK, Dutta AK, Kim C, Saleh MA, Islam MA, Acharjee UK, Kim B. Biochemical and molecular docking-based strategies of Acalypha indica and Boerhavia diffusa extract by targeting bacterial strains and cancer proteins. J Biomol Struct Dyn 2023:1-18. [PMID: 38146734 DOI: 10.1080/07391102.2023.2297011] [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: 07/28/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
Antibiotic-resistant microbes have emerged around the world, presenting a risk to health. Plant-derived drugs have become a potential source for the production of antibiotic-resistant drugs and cancer therapies. In this study, we investigated the antibacterial, cytotoxic and antioxidant properties of Acalypha indica and Boerhavia diffusa, and conducted in silico molecular docking experiments against EGFR and VEGFR-2 proteins. The metabolic extract of A. indica inhibited Streptococcus iniae and Staphylococcus sciuri with inhibition zones of 21.66 ± 0.57 mm and 20.33 ± 0.57 mm, respectively. The B. diffusa leaf extract produced inhibition zones of 20.3333 ± 0.5773 mm and 20.33 ± 0.57 mm against Streptococcus iniae and Edwardsiella anguillarum, respectively. A. indica and B. diffusa extracts had toxicities of 162.01 μg/ml and 175.6 μg/ml, respectively. Moreover, B. diffusa (IC50 =154.42 µg/ml) leaf extract exhibited moderately higher antioxidant activity compared with the A. indica (IC50 = 218.97 µg/ml) leaf extract. Multiple interactions were observed at Leu694, Met769 and Leu820 sites for EGFR and at Asp1046 and Cys1045 sites for VEGFR during the molecular docking study. CID-235030, CID-70825 and CID-156619353 had binding energies of -7.6 kJ/mol, -7.5 kJ/mol and -7.6 kJ/mol, respectively, with EGFR protein. VEGFR-2 protein had docking energies of -7.5 kJ/mol, -7.6 kJ/mol and -7.3 kJ/mol, respectively, for CID-6420353, CID-156619353 and CID-70825 compounds. The MD simulation trajectories revealed the hit compound; CID-235030 and EGFR complex, CID-6420353 and VEGFR-2 exhibit stable profile in the root mean square deviation (RMSD), radius of gyration (Rg), solvent accessible surface area (SASA), hydrogen bond and root mean square fluctuation (RMSF) and the binding free energy by MM-PBSA method. This study indicates that methanol extracts of A. indica and B. diffusa may play a crucial role in developing antibiotic-resistant and cancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mst Sharmin Sultana Shimu
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh, India
| | - Gobindo Kumar Paul
- Department of Genetic engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh, India
| | - Amit Kumar Dutta
- Department of Microbiology, University of Rajshahi, Rajshahi, Bangladesh, India
| | - Changhyun Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, Korea
| | - Md Abu Saleh
- Department of Genetic engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh, India
| | - Md Asadul Islam
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh, India
| | - Uzzal Kumar Acharjee
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh, India
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, Korea
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Wang S, Li Y, Lin X, Fu X, Zhong H, Ren K, Liu C, Yao W. Rapid Screening of Phenolic Compounds with Anti-Enteritis Activity from Camellia oleifera Oil Using a Smurf Drosophila Model and Molecular Docking Methods. Molecules 2023; 29:76. [PMID: 38202658 PMCID: PMC10780214 DOI: 10.3390/molecules29010076] [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: 10/31/2023] [Revised: 12/03/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Screening and identifying the active compounds in foods are important for the development and utilization of functional foods. In this study, the anti-enteritis activity of ethanol extract from Camellia oleifera oil (PECS) was quickly evaluated using a Smurf Drosophila model and the metabolomics approach, combined with molecular docking techniques, were performed to rapidly screen and identify compounds with potential anti-enteritis activity in PECS. PECS showed good anti-enteritis activity and inhibited the activity of 5-lipoxygenase (LOX), cyclooxygenase 2 (COX-2) and inducible nitric oxide synthase (iNOS). In particular, wighteone and p-octopamine were newly identified in C. oleifera oil and were proven to have good anti-enteritis activity. The inhibitory activity of kaempferitrin (IC50 = 0.365 mmol L-1) was higher than that of wighteone (IC50 = 0.424 mmol L-1) and p-octopamine (IC50 = 0.402 mmol L-1). Of note, the IC50 value of salazosulfapyridine was 0.810 mmol L-1. Inhibition of LOX activity is likely one of the anti-enteritis mechanisms of PECS. These new findings lay the foundation for further investigations into the underlying mechanisms of anti-enteritis activity in C. oleifera oil.
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Affiliation(s)
- Shuhao Wang
- Hunan Provincial Key Laboratory of Forest Edible Resources Safety and Processing Utilization, Central South University of Forestry and Technology, Changsha 410004, China
- Commodity Quality Inspection Institute of Hunan Province, Changsha 410004, China
| | - Yang Li
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xin Lin
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xiangjin Fu
- Hunan Provincial Key Laboratory of Forest Edible Resources Safety and Processing Utilization, Central South University of Forestry and Technology, Changsha 410004, China
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Haiyan Zhong
- Hunan Provincial Key Laboratory of Forest Edible Resources Safety and Processing Utilization, Central South University of Forestry and Technology, Changsha 410004, China
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Kangzi Ren
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Cheng Liu
- Yi-Feng Agriculture and Forestry Technology Co., Ltd., Shaoyang 422300, China
| | - Wen Yao
- Hunan Ju Xiong Institute of Camellia oleifera Oil, Yueyang 414000, China;
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Alrouji M, Alhumaydhi FA, Alsayari A, Sharaf SE, Shafi S, Anwar S, Shahwan M, Atiya A, Shamsi A. Targeting Sirtuin 1 for therapeutic potential: Drug repurposing approach integrating docking and molecular dynamics simulations. PLoS One 2023; 18:e0293185. [PMID: 38117829 PMCID: PMC10732437 DOI: 10.1371/journal.pone.0293185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/08/2023] [Indexed: 12/22/2023] Open
Abstract
Identifying novel therapeutic agents is a fundamental challenge in contemporary drug development, especially in the context of complex diseases like cancer, neurodegenerative disorders, and metabolic syndromes. Here, we present a comprehensive computational study to identify potential inhibitors of SIRT1 (Sirtuin 1), a critical protein involved in various cellular processes and disease pathways. Leveraging the concept of drug repurposing, we employed a multifaceted approach that integrates molecular docking and molecular dynamics (MD) simulations to predict the binding affinities and dynamic behavior of a diverse set of FDA-approved drugs from DrugBank against the SIRT1. Initially, compounds were shortlisted based on their binding affinities and interaction analyses to identify safe and promising binding partners for SIRT1. Among these candidates, Doxercalciferol and Timiperone emerged as potential candidates, displaying notable affinity, efficiency, and specificity towards the binding pocket of SIRT1. Extensive evaluation revealed that these identified compounds boast a range of favorable biological properties and prefer binding to the active site of SIRT1. To delve deeper into the interactions, all-atom MD simulations were conducted for 500 nanoseconds (ns). These simulations assessed the conformational dynamics, stability, and interaction mechanism of the SIRT1-Doxercalciferol and SIRT1-Timiperone complexes. The MD simulations illustrated that the SIRT1-Doxercalciferol and SIRT1-Timiperone complexes maintain stability over a 500 ns trajectory. These insightful outcomes propose that Doxercalciferol and Timiperone hold promise as viable scaffolds for developing potential SIRT1 inhibitors, with implications for tackling complex diseases such as cancer, neurodegenerative disorders, and metabolic syndromes.
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Affiliation(s)
- Mohammed Alrouji
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra, Saudi Arabia
| | - Fahad A. Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Abdulrhman Alsayari
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Abha, Saudi Arabia
- Complementary and Alternative Medicine Unit, King Khalid University (KKU), Abha, Saudi Arabia
| | - Sharaf E. Sharaf
- Pharmaceutical Chemistry Department, College of Pharmacy Umm Al-Qura University Makkah, Makkah, Saudi Arabia
| | - Sheeba Shafi
- Department of Nursing, College of Applied Medical Sciences, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Moyad Shahwan
- Center for Medical and Bio-Allied Health Sciences, Ajman University, Ajman, UAE
| | - Akhtar Atiya
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Abha, Saudi Arabia
| | - Anas Shamsi
- Center for Medical and Bio-Allied Health Sciences, Ajman University, Ajman, UAE
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Nakao IA, Almeida TC, Cardoso Reis AC, Coutinho GG, Hermenegildo AM, Cordeiro CF, da Silva GN, Dias DF, Brandão GC, Pinto Braga SF, de Souza TB. Discovery of a new dihydroeugenol-chalcone hybrid with cytotoxic and anti-migratory potential: A dual-action hit for cancer therapeutics. Bioorg Med Chem 2023; 96:117516. [PMID: 37944413 DOI: 10.1016/j.bmc.2023.117516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
Cancer still represents a serious public health problem and one of the main problems related to the worsening of this disease is the ability of some tumors to develop metastasis. In this work, we synthesized a new series of chalcones and isoxazoles derived from eugenol and analogues as molecular hybrids and these compounds were evaluated against different tumor cell lines. This structural pattern was designed considering the cytotoxic potential already known for eugenol, chalcones and isoxazoles. Notably, chalcones 7, 9, 10, and 11 displayed significant activity (4.2-14.5 µM) against two cancer cell lines, surpassing the potency of the control drug doxorubicin. The reaction of chalcones with hydroxylamine hydrochloride provided the corresponding isoxazoles that were inactive against these cancer cells. The dihydroeugenol chalcone 7 showed the most promising results, demonstrating higher potency against HepG2 (CC50: 4.2 µM) and TOV-21G (CC50: 7.2 µM). Chalcone 7 was also three times less toxic than doxorubicin considering HepG2 cells, with a selectivity index greater than 11. Further investigations including clonogenic survival, cell cycle progression and cell migration assays confirmed the compelling antitumoral potential of chalcone 7, as it reduced long-term survival due to DNA fragmentation, inducing cell death and inhibiting HepG2 cells migration. Moreover, in silico studies involving docking and molecular dynamics revealed a consistent binding mode of chalcone 7 with metalloproteinases, particularly MMP-9, shedding light on its potential mechanism of action related to anti-migratory effects. These significant findings suggest the inclusion of compound 7 as a promising candidate for future studies in the field of cancer therapeutics.
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Affiliation(s)
- Izadora Amaral Nakao
- School of Pharmacy - Federal University of Ouro Preto, 35400-000 Ouro Preto, MG, Brazil
| | - Tamires Cunha Almeida
- School of Pharmacy - Federal University of Ouro Preto, 35400-000 Ouro Preto, MG, Brazil
| | | | | | | | | | | | | | - Geraldo Célio Brandão
- School of Pharmacy - Federal University of Ouro Preto, 35400-000 Ouro Preto, MG, Brazil
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Chen X, Xue B, Wahab S, Sultan A, Khalid M, Yang S. Structure-based molecular docking and molecular dynamics simulations study for the identification of dipeptidyl peptidase 4 inhibitors in type 2 diabetes. J Biomol Struct Dyn 2023:1-14. [PMID: 38100564 DOI: 10.1080/07391102.2023.2291831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023]
Abstract
Inhibition of dipeptidyl peptidase-4 (DPP4) activity has emerged as a promising therapeutic approach for the treatment of type 2 diabetes mellitus (T2DM). Bioinformatics-driven approaches have emerged as crucial tools in drug discovery. Molecular docking and molecular dynamics (MD) simulations are effective tools in drug discovery, as they reduce the time and cost associated with experimental screening. In this study, we employed structure-assisted in-silico methods, including molecular docking and MD simulations, to identify SRT2183, a small molecule that may potentially inhibit the activity of DPP4 enzyme. The interaction between the small molecule "SRT2183" and DPP4 exhibited a binding affinity of -9.9 Kcal/Mol, leading to the formation of hydrogen bonds with the amino acid residues MET348, SER376, and THR351 of DPP4. The MD simulations over a period of 100 ns indicated stable protein-ligand interactions, with no significant conformational rearrangements observed within the simulated timeframe. In conclusion, our results suggest that the small molecule SRT2183 may have the potential to inhibit the DPP4 enzyme and pave the way for the therapeutics of T2DM.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xi Chen
- School of Management, Guangzhou College of Technology and Business, Guangzhou, China
| | - Bin Xue
- School of Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Armiya Sultan
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Khalid
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Song Yang
- Department of Wine, Food and Molecular Biosciences, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
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B S N, P K KN, Akey KS, Sankaran S, Raman RK, Natarajan J, Selvaraj J. Vitamin D analog calcitriol for breast cancer therapy; an integrated drug discovery approach. J Biomol Struct Dyn 2023; 41:11017-11043. [PMID: 37054526 DOI: 10.1080/07391102.2023.2199866] [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: 07/25/2022] [Accepted: 12/11/2022] [Indexed: 04/15/2023]
Abstract
As breast cancer remains leading cause of cancer death globally, it is essential to develop an affordable breast cancer therapy in underdeveloped countries. Drug repurposing offers potential to address gaps in breast cancer treatment. Molecular networking studies were performed for drug repurposing approach by using heterogeneous data. The PPI networks were built to select the target genes from the EGFR overexpression signaling pathway and its associated family members. The selected genes EGFR, ErbB2, ErbB4 and ErbB3 were allowed to interact with 2637 drugs, leads to PDI network construction of 78, 61, 15 and 19 drugs, respectively. As drugs approved for treating non cancer-related diseases or disorders are clinically safe, effective, and affordable, these drugs were given considerable attention. Calcitriol had shown significant binding affinities with all four receptors than standard neratinib. The RMSD, RMSF, and H-bond analysis of protein-ligand complexes from molecular dynamics simulation (100 ns), confirmed the stable binding of calcitriol with ErbB2 and EGFR receptors. In addition, MMGBSA and MMP BSA also affirmed the docking results. These in-silico results were validated with in-vitro cytotoxicity studies in SK-BR-3 and Vero cells. The IC50 value of calcitriol (43.07 mg/ml) was found to be lower than neratinib (61.50 mg/ml) in SK-BR-3 cells. In Vero cells the IC50 value of calcitriol (431.05 mg/ml) was higher than neratinib (404.95 mg/ml). It demonstrates that calcitriol suggestively downregulated the SK-BR-3 cell viability in a dose-dependent manner. These implications revealed calcitriol has shown better cytotoxicity and decreased the proliferation rate of breast cancer cells than neratinib.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nagaraj B S
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamilnadu, India
| | - Krishnan Namboori P K
- Amrita Molecular Modeling and Synthesis (AMMAS) Research lab, Amrita Vishwavidyapeetham, Coimbatore, Tamilnadu, India
| | - Krishna Swaroop Akey
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamilnadu, India
| | - Sathianarayanan Sankaran
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Karpagam Academy of Higher Education, Coimbatore, Tamilnadu, India
| | - Rajesh Kumar Raman
- Department of Pharmaceutical Biotechnology, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamilnadu, India
| | - Jawahar Natarajan
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamilnadu, India
| | - Jubie Selvaraj
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamilnadu, India
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Casson CL, John SA, Ferrall-Fairbanks MC. Mathematical modeling of cardio-oncology: Modeling the systemic effects of cancer therapeutics on the cardiovascular system. Semin Cancer Biol 2023; 97:30-41. [PMID: 37979714 DOI: 10.1016/j.semcancer.2023.11.004] [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: 11/15/2022] [Revised: 08/25/2023] [Accepted: 11/12/2023] [Indexed: 11/20/2023]
Abstract
Cardiotoxicity is a common side-effect of many cancer therapeutics; however, to-date there has been very little push to understand the mechanisms underlying this group of pathologies. This has led to the emergence of cardio-oncology, a field of medicine focused on understanding the effects of cancer and its treatment on the human heart. Here, we describe how mechanistic modeling approaches have been applied to study open questions in the cardiovascular system and how these approaches are being increasingly applied to advance knowledge of the underlying effects of cancer treatments on the human heart. A variety of mechanistic, mathematical modeling techniques have been applied to explore the link between common cancer treatments, such as chemotherapy, radiation, targeted therapy, and immunotherapy, and cardiotoxicity, nevertheless there is limited coverage in the different types of cardiac dysfunction that may be associated with these treatments. Moreover, cardiac modeling has a rich heritage of mathematical modeling and is well suited for the further development of novel approaches for understanding the cardiotoxicities associated with cancer therapeutics. There are many opportunities to combine mechanistic, bottom-up approaches with data-driven, top-down approaches to improve personalized, precision oncology to better understand, and ultimately mitigate, cardiac dysfunction in cancer patients.
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Affiliation(s)
- Camara L Casson
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Sofia A John
- Department of Statistics, University of Florida, Gainesville, FL 32611, USA
| | - Meghan C Ferrall-Fairbanks
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA; University of Florida Health Cancer Center, University of Florida, Gainesville, FL 32611, USA.
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Li X, Shi R, Yan L, Chu W, Sun R, Zheng B, Wang S, Tan H, Wang X, Gao Y. Natural product rhynchophylline prevents stress-induced hair graying by preserving melanocyte stem cells via the β2 adrenergic pathway suppression. NATURAL PRODUCTS AND BIOPROSPECTING 2023; 13:54. [PMID: 38036925 PMCID: PMC10689686 DOI: 10.1007/s13659-023-00421-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
Norepinephrine (NA), a stress hormone, can accelerate hair graying by binding to β2 adrenergic receptors (β2AR) on melanocyte stem cells (McSCs). From this, NA-β2AR axis could be a potential target for preventing the stress effect. However, identifying selective blockers for β2AR has been a key challenge. Therefore, in this study, advanced computer-aided drug design (CADD) techniques were harnessed to screen natural molecules, leading to the discovery of rhynchophylline as a promising compound. Rhynchophylline exhibited strong and stable binding within the active site of β2AR, as verified by molecular docking and dynamic simulation assays. When administered to cells, rhynchophylline effectively inhibited NA-β2AR signaling. This intervention resulted in a significant reduction of hair graying in a stress-induced mouse model, from 28.5% to 8.2%. To gain a deeper understanding of the underlying mechanisms, transcriptome sequencing was employed, which revealed that NA might disrupt melanogenesis by affecting intracellular calcium balance and promoting cell apoptosis. Importantly, rhynchophylline acted as a potent inhibitor of these downstream pathways. In conclusion, the study demonstrated that rhynchophylline has the potential to mitigate the negative impact of NA on melanogenesis by targeting β2AR, thus offering a promising solution for preventing stress-induced hair graying.
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Affiliation(s)
- Xinxin Li
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
- Department of Anesthesiology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, China
- Center for Child Care and Mental Health, Shenzhen Children's Hospital Affiliated to Shantou University Medical College, Shenzhen, 518026, China
| | - Runlu Shi
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Lingchen Yan
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Weiwei Chu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
- Department of Anesthesiology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, China
| | - Ruishuang Sun
- Department of Plastic and Reconstructive Surgery, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Binkai Zheng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Shuai Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
- The Yonghe Medical Beauty Clinic Department, Guangzhou, 510630, China
| | - Hui Tan
- Center for Child Care and Mental Health, Shenzhen Children's Hospital Affiliated to Shantou University Medical College, Shenzhen, 518026, China.
| | - Xusheng Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China.
| | - Ying Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China.
- Department of Anesthesiology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, China.
- Department of Anesthesiology, The First People's Hospital of Foshan, Foshan, 528000, China.
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Ballav S, Lokhande KB, Yadav RS, Ghosh P, Swamy KV, Basu S. Exploring binding mode assessment of novel kaempferol, resveratrol, and quercetin derivatives with PPAR-α as potent drug candidates against cancer. Mol Divers 2023; 27:2867-2885. [PMID: 36544031 DOI: 10.1007/s11030-022-10587-2] [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: 07/18/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Peroxisome proliferator-activated receptors (PPAR)-α, a ligand-activated transcription factor stands out to be a valuable protein target against cancer. Given that ligand binding is the crucial process for the activation of PPAR-α, fibrate class of synthetic compounds serves as potent agonist for the receptor. However, their serious side effects limit the long-term application in cancer. This emphasizes the dire need to identify new candidates that would exert desired activation by abrogating the adverse effects caused by synthetic agonists. Natural dietary products serve as an important source of drug discovery. Hence, the present study encompasses the investigation of the role of natural plant phenolic compounds: kaempferol, resveratrol, and quercetin and their 8708 derivatives by the means of computational pipeline comprising molecular docking and molecular dynamic (MD) simulation techniques. Docking calculations shortlisted potential candidates, namely 6-cinnamylchrysin (6-CC), resveratrol potassium-4-sulfate (RPS) and 6-[2-(3,4-Dihydroxyphenyl)-5-hydroxy-4-oxochromen-7-yl]oxyhexyl nitrate (DHOON), and derivatives of kaempferol, resveratrol, and quercetin, respectively. 6-CC, RPS, and DHOON manifested better affinities of - 32.83 kcal/mol (Ala333, Lys358, His440), - 27.22 kcal/mol (Tyr314, Met355), and - 30.18 kcal/mol (Ser280, Tyr314, Ala333), respectively, and were found to act as good stimulants for PPAR-α. Among these three compounds, 6-CC caused relatively least deviations and fluctuations analyzed through MD simulation which judiciously held responsible to attain most favorable interaction with PPAR-α. Followed by the binding free energy (ΔG) calculations using MM-GBSA confirmed the key role of 6-CC toward PPAR-α. The compound 6-CC also achieved high drug-likeness and pharmacokinetic properties. Thus, these findings stipulate new drug leads for PPAR-α receptor which abets a way to develop new anti-cancer drugs.
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Affiliation(s)
- Sangeeta Ballav
- Cancer and Translational Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
| | - Kiran Bharat Lokhande
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, 411033, Maharashtra, India
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, 201314, India
| | - Rohit Singh Yadav
- Cancer and Translational Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, 411033, Maharashtra, India
| | - Payel Ghosh
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - K V Swamy
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, 411033, Maharashtra, India
- Bioinformatics Research Group, MIT School of Bioengineering Science & Research, MIT Art, Design and Technology University, Pune, Maharashtra, 412201, India
| | - Soumya Basu
- Cancer and Translational Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India.
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Balogun FO, Singh K, Rampadarath A, Akoonjee A, Naidoo K, Sabiu S. Cheminformatics identification of modulators of key carbohydrate-metabolizing enzymes from C. cujete for type-2 diabetes mellitus intervention. J Diabetes Metab Disord 2023; 22:1299-1317. [PMID: 37969920 PMCID: PMC10638353 DOI: 10.1007/s40200-023-01249-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 06/07/2023] [Indexed: 11/17/2023]
Abstract
Purpose The therapeutic use of oral hypoglycaemic agents in the management of type-2 diabetes mellitus (T2DM) is without adverse effects; thus, calls for alternative and novel candidates from natural products in medicinal plants. Method The study explored molecular docking and molecular dynamics (MD) simulation approaches to identify key antidiabetic metabolites from Crescentia cujete. Results Molecular docking results identified four and/or five best compounds against each target enzyme (alpha-glucosidase, dipeptidyl peptidase-IV, aldose reductase, and protein tyrosine phosphatase-1B (PTP-1B)) implicated in diabetes. The resulting complexes (except against PTP-1B) had higher docking scores above respective standards (acarbose, Diprotin A, ranirestat). The MD simulation results revealed compounds such as benzoic acid (-48.414 kcal/mol) and phytol (-45.112 kcal/mol) as well as chlorogenic acid (-42.978 kcal/mol) and naringenin (-31.292 kcal/mol) had higher binding affinities than the standards [acarbose (-28.248 kcal/mol), ranirestat (-21.042 kcal/mol)] against alpha-glucosidase and aldose reductase, respectively while Diprotin A (-45.112 kcal/mol) and ursolic acid (-18.740 kcal/mol) presented superior binding affinities than the compounds [luteolin (-41.957 kcal/mol and naringenin (-16.518 kcal/mol)] against DPP-IV and PTP-1B respectively. Conclusion While isoflavone (alpha-glucosidase), xylocaine (DPP-IV), luteolin (aldose reductase,) and chlorogenic acid (PTP-1B) were affirmed as the best inhibitors of respective enzyme targets, luteolin, and chlorogenic acid may be suggested and proposed as probable candidates against T2DM and related retinopathy complication based on their structural stability, compactness and affinity for three (DPP-IV, aldose reductase, and PTP-1B) of the four targets investigated. Further studies are warranted in vitro and in vivo on the antihyperglycaemic effects of these drug candidates. Supplementary Information The online version contains supplementary material available at 10.1007/s40200-023-01249-7.
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Affiliation(s)
- Fatai Oladunni Balogun
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000 South Africa
| | - Karishma Singh
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000 South Africa
- Department of Nature Conservation, Mangosuthu University of Technology, Mangosuthu, South Africa
| | - Athika Rampadarath
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000 South Africa
| | - Ayesha Akoonjee
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000 South Africa
| | - Kayleen Naidoo
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000 South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000 South Africa
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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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Dodaro A, Pavan M, Menin S, Salmaso V, Sturlese M, Moro S. Thermal titration molecular dynamics (TTMD): shedding light on the stability of RNA-small molecule complexes. Front Mol Biosci 2023; 10:1294543. [PMID: 38028536 PMCID: PMC10679717 DOI: 10.3389/fmolb.2023.1294543] [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: 09/14/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Ribonucleic acids are gradually becoming relevant players among putative drug targets, thanks to the increasing amount of structural data exploitable for the rational design of selective and potent binders that can modulate their activity. Mainly, this information allows employing different computational techniques for predicting how well would a ribonucleic-targeting agent fit within the active site of its target macromolecule. Due to some intrinsic peculiarities of complexes involving nucleic acids, such as structural plasticity, surface charge distribution, and solvent-mediated interactions, the application of routinely adopted methodologies like molecular docking is challenged by scoring inaccuracies, while more physically rigorous methods such as molecular dynamics require long simulation times which hamper their conformational sampling capabilities. In the present work, we present the first application of Thermal Titration Molecular Dynamics (TTMD), a recently developed method for the qualitative estimation of unbinding kinetics, to characterize RNA-ligand complexes. In this article, we explored its applicability as a post-docking refinement tool on RNA in complex with small molecules, highlighting the capability of this method to identify the native binding mode among a set of decoys across various pharmaceutically relevant test cases.
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Affiliation(s)
| | | | | | | | | | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
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Reza R, Morshed N, Samdani MN, Reza MS. Pharmacophore mapping approach to find anti-cancer phytochemicals with metformin-like activities against transforming growth factor (TGF)-beta receptor I kinase: An in silico study. PLoS One 2023; 18:e0288208. [PMID: 37943796 PMCID: PMC10635513 DOI: 10.1371/journal.pone.0288208] [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: 03/15/2023] [Accepted: 06/21/2023] [Indexed: 11/12/2023] Open
Abstract
The most frequently prescribed first-line treatment for type II diabetes mellitus is metformin. Recent reports asserted that this diabetes medication can also shield users from cancer. Metformin induces cell cycle arrest in cancer cells. However, the exact mechanism by which this occurs in the cancer system is yet to be elucidated. Here, we investigated the impact of metformin on cell cycle arrest in cancer cells utilizing transforming growth factor (TGF)-beta pathway. TGF-ß pathway has significant effect on cell progression and growth. In order to gain an insight on the underlying molecular mechanism of metformin's effect on TGF beta receptor 1 kinase, molecular docking was performed. Metformin was predicted to interact with transforming growth factor (TGF)-beta receptor I kinase based on molecular docking and molecular dynamics simulations. Furthermore, pharmacophore was generated for metformin-TGF-ßR1 complex to hunt for novel compounds having similar pharmacophore as metformin with enhanced anti-cancer potentials. Virtual screening with 29,000 natural compounds from NPASS database was conducted separately for the generated pharmacophores in Ligandscout® software. Pharmacophore mapping showed 60 lead compounds for metformin-TGF-ßR1 complex. Molecular docking, molecular dynamics simulation for 100 ns and ADMET analysis were performed on these compounds. Compounds with CID 72473, 10316977 and 45140078 showed promising binding affinities and formed stable complexes during dynamics simulation with aforementioned protein and thus have potentiality to be developed into anti-cancer medicaments.
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Affiliation(s)
- Rumman Reza
- Department of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Niaz Morshed
- Department of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | | | - Md. Selim Reza
- Department of Pharmaceutical Technology, University of Dhaka, Dhaka, Bangladesh
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Roopashree B, Mahesh B, Ramu R, Rekha ND, Manjula SN, Preethi G, Gayathri V. An insight into the cytotoxic, antimicrobial, antioxidant, and biocontrol perspective of novel Iron(III) complexes of substituted benzimidazoles: Inhibition kinetics and molecular simulations. J Biomol Struct Dyn 2023:1-17. [PMID: 37794762 DOI: 10.1080/07391102.2023.2263569] [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: 05/15/2023] [Accepted: 09/17/2023] [Indexed: 10/06/2023]
Abstract
Mononuclear complexes [FeCl3L2(OH2)] (L = L1, L2) were designed and synthesized by combining FeCl3 with 2-(3'-Aminophenylbenzimidazole) (L1) and 2-[(3'-N-Salicylidinephenyl)benzimidazole] (L2) and were characterized by physico-analytical strategies. The redox properties of the complexes were disclosed by the cyclic voltammetric method. Further, the interactions of complexes with proteins were studied by performing molecular docking engaging protein models of common cancer therapeutic targets to foresee their affinity to bind to these proteins. The complexes evidenced better protein-ligand docking (-8.4 and -9.0 kcal mol-1) and higher binding energies than their ligands. However, the L1 complex displayed improved binding free energy (-33.576 ± 1.01 kcal mol-1) compared to the other complexes and individual ligands. These compounds were screened for in vitro cytotoxic assays against triple-negative breast cancer cell lines (MDA-MB-468 cells), anti-inflammatory, antimicrobial, and antioxidant properties. The in vitro study complemented the in silico assay; therefore, these compounds may be a viable choice for expanding anticancer therapy. Additionally, the L2 showed better biocontrol activity owing to the enhanced growth of Trichoderma and inhibited the growth of Fusarium oxysporum.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- B Roopashree
- Department of Chemistry, JSS Academy of Technical Education (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, India
| | - B Mahesh
- Department of Chemistry, JSS Academy of Technical Education (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, India
| | - N D Rekha
- Department of Bio-Technology, JSS College of Arts, Commerce and Science (Autonomous), Mysuru, India
| | - S N Manjula
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Mysuru, India
| | - G Preethi
- Department of Chemistry, JSS Academy of Technical Education (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, India
| | - V Gayathri
- Department of Studies in Chemistry, Central College Campus, Bangalore City University, Bengaluru, India
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Rehman MU, Ali A, Ansar R, Arafah A, Imtiyaz Z, Wani TA, Zargar S, Ganie SA. In Silico molecular docking and dynamic analysis of natural compounds against major non-structural proteins of SARS-COV-2. J Biomol Struct Dyn 2023; 41:9072-9088. [PMID: 36326281 DOI: 10.1080/07391102.2022.2139766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
COVID-19 has infected millions and significantly affected the global economy and healthcare systems. Despite continuous lockdowns, symptomatic management with currently available medications, and numerous vaccination drives, it is still far more difficult to control. Against COVID-19 infection, the pressure to develop vaccines and drugs has led to using some currently available medications like remdesivir, azithromycin, hydroxychloroquine and ritonavir. Understanding the importance and potential of harmless molecules to tackle SARS-COV-2, we designed the present study to identify potential natural phytocompounds. In the present study, we docked natural compounds and standard drugs against SARS-COV-2 proteins: papain-like protease, main protease and helicase. ADME/T and ProTox-II analyses were used to determine the toxicity of phytocompounds and drugs. The docking analysis revealed that podophyllotoxin gave the highest binding affinity scores of -8.1, -7.1 and -7.4 kcal/mol against PLpro, Mpro and helicase, respectively. Among the control drugs, doxycycline hydrochloride showed the highest binding affinity of -10.5, -8.4 and -8.8 kcal/mol against PLpro, Mpro and helicase. The results of this study revealed that podophyllotoxin and doxycycline hydrochloride could be promising inhibitors against SARS-Cov-2. Molecular dynamic simulations were executed for the best docked (PLpro-podophyllotoxin) complex, and the results displayed stable conformation and convergence. Energy plot results predicted a global minima average energy of -95 kcal/mol and indicated podophyllotoxin's role in stabilizing protein and making it compact and complex. FarPPI server used MM/GBSA approach to determine free binding affinity, and helicase-gallic acid complex showed the highest affinity, respectively. Therefore, it can be concluded that there is still a need for in vitro and in vivo studies to support further and validate these findings and validate these findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muneeb U Rehman
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Aarif Ali
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar, J&K, India
| | - Ruhban Ansar
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar, J&K, India
| | - Azher Arafah
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Zuha Imtiyaz
- Department of Pathology, University Maryland School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Tanveer A Wani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Seema Zargar
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Showkat A Ganie
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar, J&K, India
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Ballav S, Bhosale M, Lokhande KB, Paul MK, Padhye S, Swamy KV, Ranjan A, Basu S. Design, Synthesis, and Biological Evaluation of Novel Quercetin Derivatives as PPAR-γ Partial Agonists by Modulating Epithelial-Mesenchymal Transition in Lung Cancer Metastasis. Adv Biol (Weinh) 2023; 7:e2300036. [PMID: 37017501 DOI: 10.1002/adbi.202300036] [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: 01/23/2023] [Revised: 03/09/2023] [Indexed: 04/06/2023]
Abstract
Epithelial-to-mesenchymal transition (EMT) is responsible for driving metastasis of multiple cancer types including lung cancer. Peroxisome proliferator-activated receptor (PPAR)-γ, a ligand-activated transcription factor, controls expression of variety of genes involved in EMT. Although several synthetic compounds act as potent full agonists for PPAR-γ, their long term application is restricted due to serious adverse effects. Therefore, partial agonists involving reduced and balanced PPAR-γ activity are more effective and valued. A previous study discerned the efficacy of quercetin and its derivatives to attain favorable stabilization with PPAR-γ. Here this work is extended by synthesizing five novel quercetin derivatives (QDs) namely thiosemicarbazone (QUETSC)) and hydrazones (quercetin isonicotinic acid hydrazone (QUEINH), quercetin nicotinic acid hydrazone (QUENH), quercetin 2-furoic hydrazone (QUE2FH), and quercetin salicyl hydrazone (QUESH)) and their effects are analyzed in modulating EMT in lung cancer cell lines via PPAR-γ partial activation. QDs-treated A549 cells diminish cell proliferation strongly at nanomolar concentration compared to NCI-H460 cells. Of the five screened derivatives, QUETSC, QUE2FH, and QUESH exhibit the property of partial activation as compared to the overexpressive level of rosiglitazone. Consistently, these QDs also suppress EMT process by markedly downregulating the levels of mesenchymal markers (Snail, Slug, and zinc finger E-box binding homeobox 1) and concomitant upregulation of epithelial marker (E-cadherin).
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Affiliation(s)
- Sangeeta Ballav
- Cancer and Translational Research Centre, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, 411 033, India
| | - Mrinalini Bhosale
- Department of Chemistry, Interdisciplinary Science and Technology Research Academy, Abeda Inamdar Senior College, University of Pune, Maharashtra, 411001, India
| | - Kiran Bharat Lokhande
- Bioinformatics Research Laboratory, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, 411 033, India
| | - Manash K Paul
- Department of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Subhash Padhye
- Department of Chemistry, Interdisciplinary Science and Technology Research Academy, Abeda Inamdar Senior College, University of Pune, Maharashtra, 411001, India
| | - K Venkateswara Swamy
- Bioinformatics Research Laboratory, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, 411 033, India
- MIT School of Bioengineering Science and Research, MIT - Art, Design and Technology University, Pune, Maharashtra, 412201, India
| | - Amit Ranjan
- Cancer and Translational Research Centre, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, 411 033, India
| | - Soumya Basu
- Cancer and Translational Research Centre, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, 411 033, India
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Ruengsatra T, Meeprasert A, Rattanangkool E, Deesiri S, Srisa J, Udomnilobol U, Dunkoksung W, Chuaypen N, Kiatbumrung R, Tangkijvanich P, Vimolmangkang S, Pudhom K, Prueksaritanont T. Binding characteristics of pyrrole-scaffold hepatitis B virus capsid inhibitors and identification of novel potent compounds. RSC Adv 2023; 13:29004-29022. [PMID: 37807973 PMCID: PMC10556424 DOI: 10.1039/d3ra04720b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/24/2023] [Indexed: 10/10/2023] Open
Abstract
Hepatitis B virus (HBV) capsid assembly modulators (CAMs) are currently being evaluated in clinical trials as potential curative therapies for HBV. This study used in silico computational modeling to provide insights into the binding characteristics between the HBV core protein and two pyrrole-scaffold inhibitors, JNJ-6379 and GLP-26, both in the CAM-Normal (CAM-N) series. Molecular dynamics simulations showed that the pyrrole inhibitors displayed similar general binding-interaction patterns to NVR 3-778, another CAM-N, with hydrophobic interactions serving as the major driving force. However, consistent with their higher potency, the pyrrole inhibitors exhibited stronger nonpolar interactions with key residues in a solvent-accessible region as compared to NVR 3-778. This feature was facilitated by distinct hydrogen bond interactions of the pyrrole scaffold inhibitors with the residue 140 in chain B of the HBV core protein (L140B). Based on these findings, novel CAM-N compounds were designed to mimic the interaction with L140B residue while maximizing nonpolar interactions in the solvent-accessible region. Several 1H-pyrrole-2-carbonyl substituted pyrrolidine-based compounds with various hydrophobic side chains were synthesized and evaluated. Through analyses of the structure-activity and structure-druggability relations of a series of compounds, CU15 emerged as the most promising lead CAM-N compound, exhibiting sub-nanomolar potency and good pharmacokinetic profiles. Overall, the study demonstrated a practical approach to leverage computational methods for understanding key target binding features for rationale-based design, and for guiding the identification of novel compounds.
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Affiliation(s)
- Tanachote Ruengsatra
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Arthitaya Meeprasert
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Eakkaphon Rattanangkool
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Sirikan Deesiri
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Jakkrit Srisa
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Udomsak Udomnilobol
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Wilasinee Dunkoksung
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Natthaya Chuaypen
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University Bangkok Thailand
| | - Rattanaporn Kiatbumrung
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University Bangkok Thailand
| | - Pisit Tangkijvanich
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University Bangkok Thailand
| | - Sornkanok Vimolmangkang
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University Bangkok Thailand
| | - Khanitha Pudhom
- Department of Chemistry, Faculty of Science, Chulalongkorn University Bangkok Thailand
| | - Thomayant Prueksaritanont
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
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Rama GR, Saraiva Macedo Timmers LF, Volken de Souza CF. In Silico Strategies to Predict Anti-aging Features of Whey Peptides. Mol Biotechnol 2023:10.1007/s12033-023-00887-9. [PMID: 37737930 DOI: 10.1007/s12033-023-00887-9] [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: 06/06/2023] [Accepted: 09/01/2023] [Indexed: 09/23/2023]
Abstract
We have analysed the in silico potential of bioactive peptides from cheese whey, the most relevant by-product from the dairy industry, to bind into the active site of collagenase and elastase. The peptides generated from the hydrolysis of bovine β-lactoglobulin with three proteases (trypsin, chymotrypsin, and subtilisin) were docked onto collagenase and elastase by molecular docking. The interaction models were ranked according to their free binding energy using molecular dynamics simulations, which showed that most complexes presented favourable interactions. Interactions with elastase had significantly lower binding energies than those with collagenase. Regarding the interaction site, it was found that four bioactive peptides were positioned in collagenase's active site, while six were found in elastase's active site. Among these, the most we have found one promising collagen-binding peptide produced by chymotrypsin and two for elastase, produced by subtilisin and chymotrypsin. These in silico results can be used as a tool for designing further experiments aiming at testing the in vitro potential of the peptides found in this work.
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Affiliation(s)
- Gabriela Rabaioli Rama
- Graduate Program in Biotechnology, University of Vale do Taquari-Univates, Av. Avelino Tallini, 171, Lajeado, RS, 95914-014, Brazil
| | | | - Claucia Fernanda Volken de Souza
- Graduate Program in Biotechnology, University of Vale do Taquari-Univates, Av. Avelino Tallini, 171, Lajeado, RS, 95914-014, Brazil.
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Jiao Y, Shi C, Sun Y. The use of Xuanbai Chengqi decoction on monkeypox disease through the estrone-target AR interaction. Front Microbiol 2023; 14:1234817. [PMID: 37808322 PMCID: PMC10553791 DOI: 10.3389/fmicb.2023.1234817] [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: 06/05/2023] [Accepted: 08/16/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction After COVID-19, there was an outbreak of a new infectious disease caused by monkeypox virus. So far, no specific drug has been found to treat it. Xuanbai Chengqi decoction (XBCQD) has shown effects against a variety of viruses in China. Methods We searched for the active compounds and potential targets for XBCQD from multiple open databases and literature. Monkeypox related targets were searched out from the OMIM and GeneCards databases. After determining the assumed targets of XBCQD for monkeypox treatment, we built the PPI network and used R for GO enrichment and KEGG pathway analysis. The interactions between the active compounds and the hub targets were investigated by molecular docking and molecular dynamics (MD) simulations. Results In total, 5 active compounds and 10 hub targets of XBCQD were screened out. GO enrichment and KEGG analysis demonstrated that XBCQD plays a therapeutic role in monkeypox mainly by regulating signaling pathways related to viral infection and inflammatory response. The main active compound estrone binding to target AR was confirmed to be the best therapy choice for monkeypox. Discussion This study systematically explored the interactions between the bioactive compounds of XBCQD and the monkeypox-specific XBCQD targets using network pharmacological methods, bioinformatics analyses and molecular simulations, suggesting that XBCQD could have a beneficial therapeutic effect on monkeypox by reducing the inflammatory damage and viral replication via multiple pathways. The use of XBCQD on monkeypox disease was confirmed to be best worked through the estrone-target AR interaction. Our work could provide evidence and guidance for further research on the treatment of monkeypox disease.
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Affiliation(s)
- Yanqi Jiao
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, China
| | - Chengcheng Shi
- School of Science/State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (Shenzhen), Shenzhen, China
| | - Yao Sun
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, China
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Si X, Lyu S, Hussain Q, Ye H, Huang C, Li Y, Huang J, Chen J, Wang K. Analysis of Delta(9) fatty acid desaturase gene family and their role in oleic acid accumulation in Carya cathayensis kernel. FRONTIERS IN PLANT SCIENCE 2023; 14:1193063. [PMID: 37771493 PMCID: PMC10523321 DOI: 10.3389/fpls.2023.1193063] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/14/2023] [Indexed: 09/30/2023]
Abstract
Carya cathayensis, commonly referred to as Chinese hickory, produces nuts that contain high-quality edible oils, particularly oleic acid (18:1). It is known that stearoyl-ACP desaturase (SAD) is the first key step converting stearic acid (C18:0, SA) to oleic acid (C18:1, OA) in the aminolevulinic acid (ALA) biosynthetic pathway and play an important role in OA accumulation. Thus far, there is little information about SAD gene family in C. cathayensis and the role of individual members in OA accumulation. This study searched the Chinese Hickory Genome Database and identified five members of SAD genes, designated as CcSADs, at the whole genome level through the comparison with the homologous genes from Arabidopsis. RNA-Seq analysis showed that CcSSI2-1, CcSSI2-2, and CcSAD6 were highly expressed in kernels. The expression pattern of CcSADs was significantly correlated with fatty acid accumulation during the kernel development. In addition, five full-length cDNAs encoding SADs were isolated from the developing kernel of C. cathayensis. CcSADs-green fluorescent protein (GFP) fusion construct was infiltrated into tobacco epidermal cells, and results indicated their chloroplast localization. The catalytic function of these CcSADs was further analyzed by heterologous expression in Saccharomyces cerevisiae, Nicotiana benthamiana, and walnut. Functional analysis demonstrated that all CcSADs had fatty acid desaturase activity to catalyze oleic acid biosynthesis. Some members of CcSADs also have strong substrate specificity for 16:0-ACP to synthesize palmitoleic acid (C16:1, PA). Our study documented SAD gene family in C. cathayensis and the role of CcSSI2-1, CcSSI2-2, and CcSAD6 in OA accumulation, which could be important for future improvement of OA content in this species via genetic manipulation.
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Affiliation(s)
- Xiaolin Si
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Zhejiang, China
| | - Shiheng Lyu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Zhejiang, China
| | - Quaid Hussain
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Hongyu Ye
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Zhejiang, China
| | - Chunying Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Zhejiang, China
| | - Yan Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Zhejiang, China
| | - Jianqin Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Zhejiang, China
| | - Jianjun Chen
- Mid-Florida Research and Education Center, Environmental Horticulture Department, Institute of Food and Agricultural Sciences, University of Florida, Apopka, FL, United States
| | - Ketao Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Zhejiang, China
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