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Ochiai K, Yonezawa R, Fujii S. Structural Development of Androgen Receptor Antagonists Using Phenylferrocene Framework as a Hydrophobic Pharmacophore. ChemMedChem 2024; 19:e202400040. [PMID: 38291942 DOI: 10.1002/cmdc.202400040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/01/2024]
Abstract
We previously identified nitrophenylferrocenes and cyanophenylferrocenes as promising lead structures of novel androgen receptor (AR) antagonists, based on the structural similarity between ferrocene and the steroidal skeleton. In the present research, we explored the structure-activity relationship (SAR) of phenylferrocene derivatives. Introduction of a hydrophobic substituent such as a chlorine atom at the 2-position or 3-position of phenylferrocene derivatives significantly increased the antagonistic activity toward wild-type AR, and among the synthesized compounds, 3-chloro-4-cyanophenylferrocene (29) exhibited the most potent anti-proliferative activity toward the androgen-dependent growth of SC-3 cells expressing wild-type AR (IC50 14 nM). Like conventional antiandrogens such as hydroxyflutamide, the major active metabolite of flutamide, compound 29 exhibited agonistic activity toward T877A-AR, a mutant AR expressed in human prostate cancer cell line LNCaP. Notably, however, the 2-chloro isomer 27 showed potent antagonistic activity toward wild-type AR (IC50 49 nM) and also exhibited antagonistic activity toward T877A-AR. Our SAR data should prove helpful for the development of new-generation AR antagonists based on phenylferrocene as candidate agents to treat drug-resistant prostate cancer.
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Affiliation(s)
- Kotaro Ochiai
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Ryo Yonezawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Shinya Fujii
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
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2
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Chakraborty P, Lubna S, Bhuin S, K. D, Chakravarty M, Jamma T, Yogeeswari P. Targeting hexokinase 2 for oral cancer therapy: structure-based design and validation of lead compounds. Front Pharmacol 2024; 15:1346270. [PMID: 38529190 PMCID: PMC10961359 DOI: 10.3389/fphar.2024.1346270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/20/2024] [Indexed: 03/27/2024] Open
Abstract
The pursuit of small molecule inhibitors targeting hexokinase 2 (HK2) has significantly captivated the field of cancer drug discovery. Nevertheless, the creation of selective inhibitors aimed at specific isoforms of hexokinase (HK) remains a formidable challenge. Here, we present a multiple-pharmacophore modeling approach for designing ligands against HK2 with a marked anti-proliferative effect on FaDu and Cal27 oral cancer cell lines. Molecular dynamics (MD) simulations showed that the prototype ligand exhibited a higher affinity towards HK2. Complementing this, we put forth a sustainable synthetic pathway: an environmentally conscious, single-step process facilitated through a direct amidation of the ester with an amine under transition-metal-free conditions with an excellent yield in ambient temperature, followed by a column chromatography avoided separation technique of the identified lead bioactive compound (H2) that exhibited cell cycle arrest and apoptosis. We observed that the inhibition of HK2 led to the loss of mitochondrial membrane potential and increased mitophagy as a potential mechanism of anticancer action. The lead H2 also reduced the growth of spheroids. Collectively, these results indicated the proof-of-concept for the prototypical lead towards HK2 inhibition with anti-cancer potential.
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Affiliation(s)
- Purbali Chakraborty
- Department of Pharmacy, Birla Institute of Technology and Science, Hyderabad, India
- Cancer Research Group, Centre for Human Diseases Research, Birla Institute of Technology and Science, Hyderabad, India
| | - Syeda Lubna
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - Shouvik Bhuin
- Department of Chemistry, Birla Institute of Technology and Science, Hyderabad, India
| | - Deepika K.
- Department of Pharmacy, Birla Institute of Technology and Science, Hyderabad, India
| | - Manab Chakravarty
- Department of Chemistry, Birla Institute of Technology and Science, Hyderabad, India
| | - Trinath Jamma
- Cancer Research Group, Centre for Human Diseases Research, Birla Institute of Technology and Science, Hyderabad, India
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - Perumal Yogeeswari
- Department of Pharmacy, Birla Institute of Technology and Science, Hyderabad, India
- Cancer Research Group, Centre for Human Diseases Research, Birla Institute of Technology and Science, Hyderabad, India
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Laskowska A, Pacuła-Miszewska AJ, Obieziurska-Fabisiak M, Jastrzębska A, Długosz-Pokorska A, Gach-Janczak K, Ścianowski J. Synthesis of New Chiral β-Carbonyl Selenides with Antioxidant and Anticancer Activity Evaluation-Part I. Materials (Basel) 2024; 17:899. [PMID: 38399148 PMCID: PMC10890689 DOI: 10.3390/ma17040899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024]
Abstract
A series of unsymmetrical phenyl β-carbonyl selenides with o-amido function substituted on the nitrogen atom with chiral alkyl groups was obtained. The compounds form a series of enantiomeric and diastereomeric pairs and present the first examples of this type of chiral Se derivatives. All obtained selenides were further evaluated as antioxidants and anticancer agents to define the influence of the particular stereochemistry of the attached functional groups on the bioactivity of the molecules. The highest H2O2 reduction potential was observed for N-(cis-2-hydroxy-1-indanyl)-2-((2-oxopropyl)selanyl)benzamide, and the best radical scavenging properties for N-(-1-hydroxy-2-butanyl)-2-((2-oxopropyl)selanyl)benzamide. Also, both enantiomers of the N-(1-hydroxy-2-butanyl) selenide expressed the highest cytotoxic potential towards human promyelocytic leukemia HL-60 cell line with similar IC50 values 14.4 ± 0.5 and 16.2 ± 1.1 µM, respectively. On the other hand, breast cancer cell line MCF-7 was most sensitive to N-((R)-(-)-1-hydroxy-2-butanyl)- 2-((2-oxopropyl)selanyl)benzamide (IC50 of 35.7 ± 0.6 µM). The structure-activity dependence of the obtained Se derivatives was discussed, and the most potent compounds were selected.
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Affiliation(s)
- Anna Laskowska
- Department of Organic Chemistry, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Street, 87-100 Torun, Poland; (A.L.); (A.J.P.-M.); (M.O.-F.)
| | - Agata J. Pacuła-Miszewska
- Department of Organic Chemistry, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Street, 87-100 Torun, Poland; (A.L.); (A.J.P.-M.); (M.O.-F.)
| | - Magdalena Obieziurska-Fabisiak
- Department of Organic Chemistry, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Street, 87-100 Torun, Poland; (A.L.); (A.J.P.-M.); (M.O.-F.)
| | - Aneta Jastrzębska
- Department of Analytical Chemistry and Applied Spectroscopy, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Street, 87-100 Torun, Poland;
| | - Angelika Długosz-Pokorska
- Department of Biomolecular Chemistry, Faculty of Medicine, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (A.D.-P.); (K.G.-J.)
| | - Katarzyna Gach-Janczak
- Department of Biomolecular Chemistry, Faculty of Medicine, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (A.D.-P.); (K.G.-J.)
| | - Jacek Ścianowski
- Department of Organic Chemistry, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Street, 87-100 Torun, Poland; (A.L.); (A.J.P.-M.); (M.O.-F.)
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Baselious F, Hilscher S, Robaa D, Barinka C, Schutkowski M, Sippl W. Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor. Int J Mol Sci 2024; 25:1358. [PMID: 38279359 PMCID: PMC10816272 DOI: 10.3390/ijms25021358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/14/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
HDAC11 is a class IV histone deacylase with no crystal structure reported so far. The catalytic domain of HDAC11 shares low sequence identity with other HDAC isoforms, which makes conventional homology modeling less reliable. AlphaFold is a machine learning approach that can predict the 3D structure of proteins with high accuracy even in absence of similar structures. However, the fact that AlphaFold models are predicted in the absence of small molecules and ions/cofactors complicates their utilization for drug design. Previously, we optimized an HDAC11 AlphaFold model by adding the catalytic zinc ion and minimization in the presence of reported HDAC11 inhibitors. In the current study, we implement a comparative structure-based virtual screening approach utilizing the previously optimized HDAC11 AlphaFold model to identify novel and selective HDAC11 inhibitors. The stepwise virtual screening approach was successful in identifying a hit that was subsequently tested using an in vitro enzymatic assay. The hit compound showed an IC50 value of 3.5 µM for HDAC11 and could selectively inhibit HDAC11 over other HDAC subtypes at 10 µM concentration. In addition, we carried out molecular dynamics simulations to further confirm the binding hypothesis obtained by the docking study. These results reinforce the previously presented AlphaFold optimization approach and confirm the applicability of AlphaFold models in the search for novel inhibitors for drug discovery.
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Affiliation(s)
- Fady Baselious
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (F.B.); (S.H.); (D.R.)
| | - Sebastian Hilscher
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (F.B.); (S.H.); (D.R.)
| | - Dina Robaa
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (F.B.); (S.H.); (D.R.)
| | - Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, 252 50 Vestec, Czech Republic;
| | - Mike Schutkowski
- Charles Tanford Protein Center, Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (F.B.); (S.H.); (D.R.)
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Saad FA, Saad JF, Siciliano G, Merlini L, Angelini C. Duchenne Muscular Dystrophy Gene Therapy. Curr Gene Ther 2024; 24:17-28. [PMID: 36411557 DOI: 10.2174/1566523223666221118160932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 11/23/2022]
Abstract
Duchenne and Becker muscular dystrophies are allelic X-linked recessive neuromuscular diseases affecting both skeletal and cardiac muscles. Therefore, owing to their single X chromosome, the affected boys receive pathogenic gene mutations from their unknowing carrier mothers. Current pharmacological drugs are palliative that address the symptoms of the disease rather than the genetic cause imbedded in the Dystrophin gene DNA sequence. Therefore, alternative therapies like gene drugs that could address the genetic cause of the disease at its root are crucial, which include gene transfer/implantation, exon skipping, and gene editing. Presently, it is possible through genetic reprogramming to engineer AAV vectors to deliver certain therapeutic cargos specifically to muscle or other organs regardless of their serotype. Similarly, it is possible to direct the biogenesis of exosomes to carry gene editing constituents or certain therapeutic cargos to specific tissue or cell type like brain and muscle. While autologous exosomes are immunologically inert, it is possible to camouflage AAV capsids, and lipid nanoparticles to evade the immune system recognition. In this review, we highlight current opportunities for Duchenne muscular dystrophy gene therapy, which has been known thus far as an incurable genetic disease. This article is a part of Gene Therapy of Rare Genetic Diseases thematic issue.
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Affiliation(s)
- Fawzy A Saad
- Department of Biology, Padua University School of Medicine, Via Trieste 75, Padova 35121, Italy
- Department of Gene Therapy, Saad Pharmaceuticals, Tornimäe 7-26, Tallinn, 10145, Estonia
| | - Jasen F Saad
- Department of Gene Therapy, Saad Pharmaceuticals, Tornimäe 7-26, Tallinn, 10145, Estonia
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, Pisa University School of Medicine, Pisa, Italy
| | - Luciano Merlini
- Department of Biomedical and Neuromotor Sciences, Bologna University School of Medicine, 40126 Bologna, Italy
| | - Corrado Angelini
- Department Neurosciences, Padova University School of Medicine, Padova, Italy
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Muhammed MT, Aki-Yalcin E. Computational Insight into the Mechanism of Action of DNA Gyrase Inhibitors; Revealing a New Mechanism. Curr Comput Aided Drug Des 2024; 20:224-235. [PMID: 37114781 DOI: 10.2174/1573409919666230419094700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 01/18/2023] [Accepted: 01/26/2023] [Indexed: 04/29/2023]
Abstract
BACKGROUND Discovery of novel antimicrobial agents is in need to deal with antibiotic resistance. Elucidating the mechanism of action for established drugs contributes to this endeavor. DNA gyrase is a therapeutic target used in the design and development of new antibacterial agents. Selective antibacterial gyrase inhibitors are available; however, resistance development against them is a big challenge. Hence, novel gyrase inhibitors with novel mechanisms are required. OBJECTIVE The aim of this study is to elucidate mode of action for existing DNA gyrase inhibitors and to pave the way towards discovery of novel inhibitors. METHODS In this study, the mechanism of action for selected DNA gyrase inhibitors available was carried out through molecular docking and molecular dynamics (MD) simulation. In addition, pharmacophore analysis, density functional theory (DFT) calculations, and computational pharmacokinetics analysis of the gyrase inhibitors were performed. RESULTS This study demonstrated that all the DNA gyrase inhibitors investigated, except compound 14, exhibit their activity by inhibiting gyrase B at a binding pocket. The interaction of the inhibitors at Lys103 was found to be essential for the binding. The molecular docking and MD simulation results revealed that compound 14 could act by inhibiting gyrase A. A pharmacophore model that consisted of the features that would help the inhibition effect was generated. The DFT analysis demonstrated 14 had relatively high chemical stability. Computational pharmacokinetics analysis revealed that most of the explored inhibitors were estimated to have good drug-like properties. Furthermore, most of the inhibitors were found to be non-mutagenic. CONCLUSION In this study, mode of action elucidation through molecular docking and MD simulation, pharmacophore model generation, pharmacokinetic property prediction, and DFT study for selected DNA gyrase inhibitors were carried out. The outcomes of this study are anticipated to contribute to the design of novel gyrase inhibitors.
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Affiliation(s)
- Muhammed Tilahun Muhammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Suleyman Demirel University, Isparta, Turkey
| | - Esin Aki-Yalcin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cyprus Health and Social Sciences University, Guzelyurt, Northern Cyprus
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Alam S, Verma S, Fatima K, Luqman S, Srivastava SK, Khan F. Pharmacophore & QSAR Guided Design, Synthesis, Pharmacokinetics and In vitro Evaluation of Curcumin Analogs for Anticancer Activity. Curr Med Chem 2024; 31:620-639. [PMID: 37132141 DOI: 10.2174/0929867330666230428162720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 02/27/2023] [Accepted: 02/27/2023] [Indexed: 05/04/2023]
Abstract
BACKGROUND As a part of our discovery of plant-based lead molecules, we provide a helpful tool, which helps in identification, designing, optimising, structural modifications, and prediction of curcumin, to discover novel analogs with enhanced bioavailability, pharmacologically safe, and anticancer potential. METHODS QSAR (Quantitative structure-activity relationship) and pharmacophore mapping models were developed and further used to design, synthesize, pharmacokinetics, and in vitro evaluation of curcumin analogs for anticancer activity. RESULTS The QSAR model yielded a high activity-descriptors relationship accuracy (r2) of 84%, a high activity prediction accuracy (rcv2) of 81%, and external set prediction accuracy of 89%. The QSAR study indicates that the five chemical descriptors were significantly correlated with anticancer activity. The important pharmacophore features identified were a hydrogen bond acceptor, a hydrophobic centre, and a negative ionizable centre. The model's predictive ability was evaluated against a set of chemically synthesized curcumin analogs. Among the tested compounds, nine curcumin analogs were found with IC50 values of 0.10 to 1.86 μg/mL. The active analogs were assessed for pharmacokinetics compliance. EGFR was identified as a potential target of synthesized active curcumin analogs through docking studies. CONCLUSION Integrating in silico design, QSAR-driven virtual screening, chemical synthesis, and experimental in vitro evaluation may lead to the early discovery of novel and promising anticancer compounds from natural sources. The developed QSAR model and common pharmacophore generation were used as a designing and predictive tool to develop novel curcumin analogs. This study may help optimize the therapeutic relationships of studied compounds for further drug development and their potential safety concerns. This study may guide compound selection and designing novel active chemical scaffolds or new combinatorial libraries of the curcumin series.
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Affiliation(s)
- Sarfaraz Alam
- Computational Biology Unit, CSIR-Central Institute of Medicinal & Aromatic Plants, P.O.-CIMAP, Lucknow 226015 (Uttar Pradesh), India
- Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad 201002 (Uttar Pradesh), India
| | - Surjeet Verma
- Medicinal Chemistry Division, CSIR-Central Institute of Medicinal & Aromatic Plants, P.O.-CIMAP, Lucknow 226015 (Uttar Pradesh), India
| | - Kaneez Fatima
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal & Aromatic Plants, P.O.-CIMAP, Lucknow 226015 (Uttar Pradesh), India
| | - Suaib Luqman
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal & Aromatic Plants, P.O.-CIMAP, Lucknow 226015 (Uttar Pradesh), India
| | - Santosh Kumar Srivastava
- Medicinal Chemistry Division, CSIR-Central Institute of Medicinal & Aromatic Plants, P.O.-CIMAP, Lucknow 226015 (Uttar Pradesh), India
| | - Feroz Khan
- Computational Biology Unit, CSIR-Central Institute of Medicinal & Aromatic Plants, P.O.-CIMAP, Lucknow 226015 (Uttar Pradesh), India
- Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad 201002 (Uttar Pradesh), India
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Amorim J, Vásquez V, Cabrera A, Martínez M, Carpio J. In Silico and In Vitro Identification of 1,8-Dihydroxy-4,5-dinitroanthraquinone as a New Antibacterial Agent against Staphylococcus aureus and Enterococcus faecalis. Molecules 2023; 29:203. [PMID: 38202786 PMCID: PMC10779913 DOI: 10.3390/molecules29010203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Increasing rates of bacterial resistance to antibiotics are a growing concern worldwide. The search for potential new antibiotics has included several natural products such as anthraquinones. However, comparatively less attention has been given to anthraquinones that exhibit functional groups that are uncommon in nature. In this work, 114 anthraquinones were evaluated using in silico methods to identify inhibitors of the enzyme phosphopantetheine adenylyltransferase (PPAT) of Staphylococcus aureus, Enterococcus faecalis, and Escherichia coli. Virtual screenings based on molecular docking and the pharmacophore model, molecular dynamics simulations, and free energy calculations pointed to 1,8-dihydroxy-4,5-dinitroanthraquinone (DHDNA) as the most promising inhibitor. In addition, these analyses highlighted the contribution of the nitro group to the affinity of this anthraquinone for the nucleotide-binding site of PPAT. Furthermore, DHDNA was active in vitro towards Gram-positive bacteria with minimum inhibitory concentration (MIC) values of 31.25 µg/mL for S. aureus and 62.5 µg/mL for E. faecalis against both antibiotic-resistant isolates and reference strains but was ineffective against E. coli. Experiments on kill-time kinetics indicated that, at the tested concentrations, DHDNA produced bacteriostatic effects on both Gram-positive bacteria. Overall, our results present DHDNA as a potential PPAT inhibitor, showing antibacterial activity against antibiotic-resistant isolates of S. aureus and E. faecalis, findings that point to nitro groups as key to explaining these results.
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Affiliation(s)
| | | | | | | | - Juan Carpio
- Unidad de Salud y Bienestar, Facultad de Bioquímica y Farmacia, Universidad Católica de Cuenca, Av. Las Américas, Cuenca 010105, Ecuador
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Žunec S, Vadlja D, Ramić A, Zandona A, Maraković N, Brekalo I, Primožič I, Katalinić M. Profiling Novel Quinuclidine-Based Derivatives as Potential Anticholinesterase Drugs: Enzyme Inhibition and Effects on Cell Viability. Int J Mol Sci 2023; 25:155. [PMID: 38203326 PMCID: PMC10778980 DOI: 10.3390/ijms25010155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
The cholinergic system, relying on the neurotransmitter acetylcholine (ACh), plays a significant role in muscle contraction, cognition, and autonomic nervous system regulation. The enzymes acetylcholinesterase, AChE, and butyrylcholinesterase, BChE, responsible for hydrolyzing ACh, can fine-tune the cholinergic system's activity and are, therefore, excellent pharmacological targets to address a range of medical conditions. We designed, synthesized, and profiled 14 N-alkyl quaternary quinuclidines as inhibitors of human AChE and BChE and analyzed their impact on cell viability to assess their safety in the context of application as potential therapeutics. Our results showed that all of the 14 tested quinuclidines inhibited both AChE and BChE in the micromolar range (Ki = 0.26 - 156.2 μM). The highest inhibition potency was observed for two bisquaternary derivatives, 7 (1,1'-(decano)bis(3-hydroxyquinuclidinium bromide)) and 14 (1,1'-(decano)bis(3-hydroxyiminoquinuclidinium bromide)). The cytotoxic effect within 7-200 μM was observed only for monoquaternary quinuclidine derivatives, especially those with the C12-C16 alkyl chain. Further analysis revealed a time-independent mechanism of action, significant LDH release, and a decrease in the cells' mitochondrial membrane potential. Taking all results into consideration, we can confirm that a quinuclidine core presents a good scaffold for cholinesterase binding and that two bisquaternary quinuclidine derivatives could be considered as candidates worth further investigations as drugs acting in the cholinergic system. On the other hand, specific cell-related effects probably triggered by the free long alkyl chain in monoquaternary quinuclidine derivatives should not be neglected in future N-alkyl quaternary quinuclidine derivative structure refinements. Such an effect and their potential to interact with other specific targets, as indicated by a pharmacophore model, open up a new perspective for future investigations of these compounds' scaffold in the treatment of specific conditions and diseases other than cholinergic system-linked disorders.
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Affiliation(s)
- Suzana Žunec
- Division of Toxicology, Institute for Medical Research and Occupational Health, Ksaverska c. 2, 10000 Zagreb, Croatia; (S.Ž.); (A.Z.); (N.M.)
| | - Donna Vadlja
- Armed Forces of the Republic of Croatia, Trg Kralja Petra Krešimira IV br. 1, 10000 Zagreb, Croatia;
| | - Alma Ramić
- Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (A.R.); (I.B.); (I.P.)
| | - Antonio Zandona
- Division of Toxicology, Institute for Medical Research and Occupational Health, Ksaverska c. 2, 10000 Zagreb, Croatia; (S.Ž.); (A.Z.); (N.M.)
| | - Nikola Maraković
- Division of Toxicology, Institute for Medical Research and Occupational Health, Ksaverska c. 2, 10000 Zagreb, Croatia; (S.Ž.); (A.Z.); (N.M.)
| | - Iva Brekalo
- Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (A.R.); (I.B.); (I.P.)
| | - Ines Primožič
- Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (A.R.); (I.B.); (I.P.)
| | - Maja Katalinić
- Division of Toxicology, Institute for Medical Research and Occupational Health, Ksaverska c. 2, 10000 Zagreb, Croatia; (S.Ž.); (A.Z.); (N.M.)
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Chen YK, Gahtani RM, Al Shahrani M, Hani U, Alshabrmi FM, Alam S, Almohaimeed HM, Basabrain AA, Shahab M, Xie MZ. Identification of potential inhibitors targeting Ebola virus VP35 protein: a computational strategy. J Biomol Struct Dyn 2023:1-13. [PMID: 38124513 DOI: 10.1080/07391102.2023.2294384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Ebola virus (EBOV) poses a severe threat as a highly infectious pathogen, causing devastating hemorrhagic fever in both humans and animals. The EBOV virus VP35 protein plays a crucial role in viral replication and exhibits the ability to suppress the host interferon cascade, leading to immune system depletion. As a potential drug target, VP35 protein inhibition holds promise for combating EBOV. To discover new drug candidates, we employed a computer-aided drug design approach, focusing on compounds capable of inhibiting VP35 protein replication. In this connection, a pharmacophore model was generated using molecular interactions between the VP35 protein and its inhibitor. ZINC and Cambridge database were screened using validated pharmacophore model. Further the compounds were filtered based on Lipinski's rule of five and subjected to MD simulation and relative binding free energy calculation. Six compounds manifest a significant docking score and strong binding interaction towards VP35 protein. MD simulations further confirmed the remarkable stability of these six complexes. Relative binding free energy calculations also showed significant ΔG value in the range of -132.3 and -49.3 kcal/mol. This study paves the way for further optimization of these compounds as potential inhibitors of VP35, facilitating subsequent experimental in vitro studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yan-Kun Chen
- School of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
- Precision Medicine R&D Center, Zhuhai Institute of Advanced Technology, Zhuhai, China
| | - Reem M Gahtani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mesfer Al Shahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Umme Hani
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha,Saudia Arabia
| | - Fahad M Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Saudi Arabia
| | - Sarfaraz Alam
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Hailah M Almohaimeed
- Department of Basic Science, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ammar A Basabrain
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Meng-Zhou Xie
- School of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
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11
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Yamkela M, Sitobo Z, Makhoba XH. In Silico Analysis of SARS-CoV-2 Non-Structural Proteins Reveals an Interaction with the Host's Heat Shock Proteins That May Contribute to Viral Replications and Development. Curr Issues Mol Biol 2023; 45:10225-10247. [PMID: 38132484 PMCID: PMC10742040 DOI: 10.3390/cimb45120638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/15/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
The non-structural protein 2 (NSP2) is an RNA-binding protein involved in coronavirus genome replication, and it often decreases human immune response to promote viral invasion and development. It is believed that the NSP2 associates itself with polyamines and heat shock proteins inside the host cell to proceed with viral development. This study aimed to investigate how the SARS-CoV-2 virus' key non-structural proteins (NSP2) utilize polyamines and heat shock proteins using a molecular docking approach and molecular dynamics (MD). ClusPro and HADDOCK servers were used for the docking and Discovery Studio, chimera, and PyMOL were used for analysis. Docking of the heat shock proteins 40 (HSP40), 70 (HSP70), and 90 (HSP90) with SARS-CoV-2 NSP2 resulted in 32, 28, and 19 interactions, respectively. Molecular dynamics revealed Arg458, Asn508, Met297, Arg301, and Trp417 as active residues, and pharmacophore modeling indicated ZINC395648, ZINC01150525, and ZINC85324008 from the zinc database as possible inhibitors for this NSP2.
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Affiliation(s)
- Mthembu Yamkela
- Department of Microbiology and Biochemistry, University of Fort Hare, Alice Campus, Alice 5700, South Africa; (M.Y.); (Z.S.)
| | - Zingisa Sitobo
- Department of Microbiology and Biochemistry, University of Fort Hare, Alice Campus, Alice 5700, South Africa; (M.Y.); (Z.S.)
| | - Xolani H. Makhoba
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa (UNISA), Florida Campus, Roodepoort 1709, South Africa
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12
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Zaib S, Rana N, Ali HS, Ur Rehman M, Awwad NS, Ibrahium HA, Khan I. Identification of potential inhibitors targeting yellow fever virus helicase through ligand and structure-based computational studies. J Biomol Struct Dyn 2023:1-18. [PMID: 38109183 DOI: 10.1080/07391102.2023.2294839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
Yellow fever is a flavivirus having plus-sensed RNA which encodes a single polyprotein. Host proteases cut this polyprotein into seven nonstructural proteins including a vital NS3 protein. The present study aims to identify the most effective inhibitor against the helicase (NS3) using different advanced ligand and structure-based computational studies. A set of 300 ligands was selected against helicase by chemical structural similarity model, which are similar to S-adenosyl-l-cysteine using infiniSee. This tool screens billions of compounds through a similarity search from in-built chemical spaces (CHEMriya, Galaxi, KnowledgeSpace and REALSpace). The pharmacophore was designed from ligands in the library that showed same features. According to the sequence of ligands, six compounds (29, 87, 99, 116, 148, and 208) were taken for pharmacophore designing against helicase protein. Subsequently, compounds from the library which showed the best pharmacophore shared-features were docked using FlexX functionality of SeeSAR and their optibrium properties were analyzed. Afterward, their ADME was improved by replacing the unfavorable fragments, which resulted in the generation of new compounds. The selected best compounds (301, 302, 303 and 304) were docked using SeeSAR and their pharmacokinetics and toxicological properties were evaluated using SwissADME. The optimal inhibitor for yellow fever helicase was 2-amino-N-(4-(dimethylamino)thiazol-2-yl)-4-methyloxazole-5-carboxamide (302), which exhibits promising potential for drug development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Nehal Rana
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Hafiz Saqib Ali
- Chemistry Research Laboratory, Department of Chemistry and the INEOS Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Mujeeb Ur Rehman
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Nasser S Awwad
- Department of Chemistry, King Khalid University, Abha, Saudi Arabia
| | - Hala A Ibrahium
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Imtiaz Khan
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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13
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Alagarsamy V, Shyam Sundar P, Raja Solomon V, Narendhar B, Sulthana MT, Rohitha K, Dhanwar S, Dharshini Aishwarya A, Murugesan S. Pharmacophore modelling-based drug repurposing approaches for monkeypox therapeutics. J Biomol Struct Dyn 2023; 41:10678-10689. [PMID: 36905675 DOI: 10.1080/07391102.2023.2188428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/05/2022] [Indexed: 03/13/2023]
Abstract
Monkeypox is a zoonotic viral disease that mainly affects tropical rainforest regions of central and west Africa, with sporadic exportations to other places. Since there is no cure, treating monkeypox with an antiviral drug developed for smallpox is currently acceptable. Our study mainly focused on finding new therapeutics to target monkeypox from existing compounds or medications. It is a successful method for discovering or developing medicinal compounds with novel pharmacological or therapeutic applications. In this study, homology modelling developed the Monkeypox VarTMPK (IMNR) structure. Ligand-based pharmacophore was generated using the best docking pose of standard ticovirimat. Further, molecular docking analysis showed compounds, tetrahydroxycurcumin, procyanidin, rutin, vicenin-2, kaempferol 3-(6''-malonylglucoside) were the top five binding energy compounds against VarTMPK (1MNR). Furthermore, we carried out MD simulations for 100 ns for the six compounds, including reference based on the binding energies and interactions. MD studies revealed that as ticovirimat interacted with residues Lys17, Ser18, and Arg45, all the above five compounds interacted with the same amino acids at the active site during docking and simulation studies. Among all the compounds, ZINC4649679 (Tetrahydroxycurcumin) was shown to have the highest binding energy -9.7 kcal/mol and also observed stable protein-ligand complex during MD studies. ADMET profile estimation showed that the docked phytochemicals were safe. However, further biological assessment through a wet lab is essential to measure the efficacy and safety of the compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- V Alagarsamy
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - P Shyam Sundar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - V Raja Solomon
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - B Narendhar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - M T Sulthana
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - Kotha Rohitha
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - Sangeeta Dhanwar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - A Dharshini Aishwarya
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - S Murugesan
- Department of Pharmacy, BITS, Pilani, Pilani, Rajasthan, India
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14
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Wang B, Meng YY, Luo MP, Wang KX, Li MY, Li DM, Zhang XG. [Advancements in virtual screening techniques for study of enzyme inhibitor compounds]. Zhongguo Zhong Yao Za Zhi 2023; 48:6533-6544. [PMID: 38212014 DOI: 10.19540/j.cnki.cjcmm.20230901.601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Enzymes are closely associated with the onset and progression of numerous diseases, making enzymes a primary target in innovative drug development. However, the challenge remains in identifying compounds that exhibit potent inhibitory effects on the target enzymes. With the continuous expansion of the total number of natural products and increasing difficulty in isolating and enriching new compounds, traditional high-throughput screening methods are finding it increasingly challenging to meet the demands of new drug development. Virtual screening, characterized by its high efficiency and low cost, has gradually become an indispensable technology in drug development. It represents a prominent example of the integration of artificial intelligence with biopharmaceuticals and is an inevitable trend in the rapid development of innovative drug screening in the future. Therefore, this article primarily focused on systematically reviewing the recent applications of virtual screening technology in the development of enzyme inhibitors and explored the prospects and advantages of using this technology in developing new drugs, aiming to provide essential theoretical insights and references for the application of related technologies in the field of new drug development.
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Affiliation(s)
- Bei Wang
- Key Laboratory of Screening and Deep Processing in New Tibetan Medicine of Gansu Province,School of Life Science and Technology, Lanzhou University of Technology Lanzhou 730050, China
| | - Ying-Ying Meng
- Key Laboratory of Screening and Deep Processing in New Tibetan Medicine of Gansu Province,School of Life Science and Technology, Lanzhou University of Technology Lanzhou 730050, China
| | - Man-Ping Luo
- Key Laboratory of Screening and Deep Processing in New Tibetan Medicine of Gansu Province,School of Life Science and Technology, Lanzhou University of Technology Lanzhou 730050, China
| | - Kang-Xu Wang
- Key Laboratory of Screening and Deep Processing in New Tibetan Medicine of Gansu Province,School of Life Science and Technology, Lanzhou University of Technology Lanzhou 730050, China
| | - Mei-Yuan Li
- Key Laboratory of Screening and Deep Processing in New Tibetan Medicine of Gansu Province,School of Life Science and Technology, Lanzhou University of Technology Lanzhou 730050, China
| | - De-Min Li
- Key Laboratory of Screening and Deep Processing in New Tibetan Medicine of Gansu Province,School of Life Science and Technology, Lanzhou University of Technology Lanzhou 730050, China
| | - Xin-Guo Zhang
- Key Laboratory of Screening and Deep Processing in New Tibetan Medicine of Gansu Province,School of Life Science and Technology, Lanzhou University of Technology Lanzhou 730050, China
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Yasir M, Park J, Lee Y, Han ET, Park WS, Han JH, Kwon YS, Lee HJ, Chun W. Discovery of GABA Aminotransferase Inhibitors via Molecular Docking, Molecular Dynamic Simulation, and Biological Evaluation. Int J Mol Sci 2023; 24:16990. [PMID: 38069313 PMCID: PMC10707509 DOI: 10.3390/ijms242316990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
γ-Aminobutyric acid aminotransferase (GABA-AT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that degrades γ-aminobutyric (GABA) in the brain. GABA is an important inhibitory neurotransmitter that plays important neurological roles in the brain. Therefore, GABA-AT is an important drug target that regulates GABA levels. Novel and potent drug development to inhibit GABA-AT is still a very challenging task. In this study, we aimed to devise novel and potent inhibitors against GABA-AT using computer-aided drug design (CADD) tools. Since the crystal structure of human GABA-AT was not yet available, we utilized a homologous structure derived from our previously published paper. To identify highly potent compounds relative to vigabatrin, an FDA-approved drug against human GABA-AT, we developed a pharmacophore analysis protocol for 530,000 Korea Chemical Bank (KCB) compounds and selected the top 50 compounds for further screening. Preliminary biological analysis was carried out for these 50 compounds and 16 compounds were further assessed. Subsequently, molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations were carried out. In the results, four predicted compounds, A07, B07, D08, and H08, were found to be highly potent and were further evaluated by a biological activity assay to confirm the results of the GABA-AT activity inhibition assay.
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Affiliation(s)
- Muhammad Yasir
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea; (M.Y.); (J.P.); (H.-J.L.)
| | - Jinyoung Park
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea; (M.Y.); (J.P.); (H.-J.L.)
| | - Yuno Lee
- Drug Information Platform Center, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea;
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea; (E.-T.H.); (J.-H.H.)
| | - Won Sun Park
- Department of Physiology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea;
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea; (E.-T.H.); (J.-H.H.)
| | - Yong-Soo Kwon
- College of Pharmacy, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Hee-Jae Lee
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea; (M.Y.); (J.P.); (H.-J.L.)
| | - Wanjoo Chun
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea; (M.Y.); (J.P.); (H.-J.L.)
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16
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Trigui E, Ben Hassen H, Zaghden H, Trigui M, Achour S. A Bioinformatic Study on the Potential Anti-Vitiligo Activity of a Carpobrotus edulis Compound. Molecules 2023; 28:7545. [PMID: 38005266 PMCID: PMC10673461 DOI: 10.3390/molecules28227545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
The plant Carpobrotus edulis has traditionally been known for its wide applications in diseases, especially vitiligo, which is characterized by patches and white macules caused by the loss of melanocytes. One of the chemical treatments for vitiligo consists mainly of skin repigmentation and usually leads to a non-durable effect by inhibiting the Janus kinase (JAK) signal transduction (STAT pathway). JAK inhibitors generally block multiple JAK tyrosine kinases, which leads to secondary effects. In this study, natural molecules from Carpobrotus edulis were extracted and tested using a structure-based drug-design approach and pharmacophore modeling. The best-fit candidate from the extracted molecules was compared to the chemical molecules used. The results indicated a similarity between the chemical and natural ligands which suggested the potential use of the natural product against vitiligo. The main finding of this research work was the discovery of a new molecule extracted from a natural plant and the detection of its anti-vitiligo activity using an in-silico approach. This method can significantly reduce the cost of searching for potential medicinal molecules.
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Affiliation(s)
- Emna Trigui
- Laboratory of Bioressources, Integrative Biology & Valorisation (BIOLIVAL), Higher Institute of Biotechnology of Monastir, Monastir University, Monastir 5000, Tunisia; (E.T.); (M.T.); (S.A.)
| | - Hanen Ben Hassen
- Laboratory of Probabilities and Statistics, Faculty of Sciences of Sfax, Sfax University, Sfax 3000, Tunisia
| | - Hatem Zaghden
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cédria, Hammam-Lif 2050, Tunisia
| | - Maher Trigui
- Laboratory of Bioressources, Integrative Biology & Valorisation (BIOLIVAL), Higher Institute of Biotechnology of Monastir, Monastir University, Monastir 5000, Tunisia; (E.T.); (M.T.); (S.A.)
| | - Sami Achour
- Laboratory of Bioressources, Integrative Biology & Valorisation (BIOLIVAL), Higher Institute of Biotechnology of Monastir, Monastir University, Monastir 5000, Tunisia; (E.T.); (M.T.); (S.A.)
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17
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Lingxia Z, Hong W, Man G, Xinzhou W, Lili W, Zhimin W, Liping D, Erping X. Rabdosichuanin C inhibits productions of pro-inflammatory mediators regulated by NF-κB signaling in LPS-stimulated RAW264.7 cells. J Cell Biochem 2023; 124:1667-1684. [PMID: 37850620 DOI: 10.1002/jcb.30474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 06/14/2023] [Accepted: 08/26/2023] [Indexed: 10/19/2023]
Abstract
Chronic pharyngitis (CP) is an inflammatory disease of the pharyngeal mucosa and its lymphatic tissues that is difficult to treat clinically. However, research on the exact therapeutic agents and molecular mechanisms of CP is still unclear. In this study, we investigated Rabdosichuanin C (RC) to attenuate lipopolysaccharide (LPS)-induced inflammatory damage in RAW264.7 cells by a combination of targeted virtual screening and in vitro activity assay and further clarified its molecular mechanism of action centering on the IκB/nuclear factor kappa B (NF-κB) pathway. Molecular docking and pharmacophore simulation methods were used to screen compounds with IκB inhibitory effects. Expression of genes and proteins related to the IκB/NF-κB signaling pathway by RC in LPS-induced inflammatory injury model of RAW264.7 cells was detected by PCR, enzyme-linked immunosorbent assay, and Western blot. The docking of RC with IκB protein showed good binding energy, and pharmacophore simulations further confirmed the active effect of RC in inhibiting IκB protein. RC intervention in LPS-induced RAW264.7 cells significantly reduced the expression levels of inflammatory factors tumor necrosis factor-α, interleukins-6, iNOS, and CD-86 at the messenger RNA and protein levels, downregulated IκB, p65 protein phosphorylation levels, and significantly inhibited IκB/NF-κB signaling pathway activation. Virtual screening provided us with an effective method to rapidly identify compounds RC that target inhibit the action of IκB, and the activity results showed that RC inhibits NF-κB signaling pathway activation. It is suggested that RC may play a role in the treatment of CP by inhibiting the IκB/NF-κB signaling pathway.
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Affiliation(s)
- Zhang Lingxia
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, Henan, China
- Engineering Technology Research Center for Comprehensive Development and Utilization of Authentic Medicinal Materials in Henan Province, Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Wu Hong
- Laboratory of Cell Imaging, Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Gong Man
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, Henan, China
- Engineering Technology Research Center for Comprehensive Development and Utilization of Authentic Medicinal Materials in Henan Province, Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Wang Xinzhou
- Laboratory of Cell Imaging, Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Wang Lili
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Wang Zhimin
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dai Liping
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, Henan, China
- Engineering Technology Research Center for Comprehensive Development and Utilization of Authentic Medicinal Materials in Henan Province, Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Xu Erping
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, Henan, China
- Engineering Technology Research Center for Comprehensive Development and Utilization of Authentic Medicinal Materials in Henan Province, Henan University of Chinese Medicine, Zhengzhou, Henan, China
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Firdaus JU, Siddiqui N, Alam O, Manaithiya A, Chandra K. Identification of novel pyrazole containing ɑ-glucosidase inhibitors: insight into pharmacophore, 3D-QSAR, virtual screening, and molecular dynamics study. J Biomol Struct Dyn 2023; 41:9398-9423. [PMID: 36376021 DOI: 10.1080/07391102.2022.2141893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022]
Abstract
Pharmacophore modelling, 3 D QSAR modelling, virtual screening, and molecular dynamics study, all-in-one combination were employed successfully design and develop an alpha-glucosidase inhibitor. To explain the structural prerequisites of biologically active components, 3 D-QSAR models were generated using the selected best hypothesis (AARRR) for compounds 55 included in the model C. The selection of 3 D-QSAR models showed that the Gaussian steric characteristic is crucial to alpha glucosidase's inhibitory potential. The alpha-glucosidase inhibitory potency of the compound is enhanced by other components, including Gaussian hydrophobic groups, Gaussian hydrogen bond acceptor or donor groups, Gaussian electrostatic characteristics, and a Gaussian steric feature. An identification of structure-activity relationships can be obtained from the developed 3 D-QSAR, C model, with R2 = 0.77 and SD = 0.02 for training set, and Q2 = 0.66, RMSE 0.02, and Pearson R = 0.81 for testing set, corresponding to elevated predictive ability. Additionally, docking and MM/GBSA experiments on 1146023 showed that it interacts with critical amino acids in the binding site when coupled with acarbose. Further, five compounds that display a high affinity for alpha-glucosidase were found, and these compounds may serve as potent leads for alpha-glucosidase inhibitor development. Biological activity will be tested for these compounds in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jannat Ul Firdaus
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Nadeem Siddiqui
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Ozair Alam
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Ajay Manaithiya
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Kailash Chandra
- Department of Biochemistry, Hamdard Institute of Medical Sciences and Research, Jamia Hamdard, New Delhi, India
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Loganathan L, Sankar J, Rajendran K, Muthusamy K. Theoretical investigation on known renin inhibitors and generation of ligand-based pharmacophore models for hypertension treatment. J Biomol Struct Dyn 2023:1-10. [PMID: 37897186 DOI: 10.1080/07391102.2023.2275186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023]
Abstract
The renin enzyme is considered a promising target for hypertension and renal diseases. Over the last three decades, several experimental and theoretical studies have been engaged in the discovery of potent renin inhibitors. The identified inhibitors that undergo clinical trials are still failing to meet the criteria of potency and safety. To date, there is no specific FDA-approved drug for renin inhibition. Our theoretical opinion describes that the most potent compounds identified in experimental studies but lacking safety and overdose issues could be solved by finding similar molecules that are stable, very active, and have no side effects, which will kick start the drug discovery process. Here, we utilized the most potent direct renin inhibitors reported earlier, followed further by our theoretical study reported in 2019. Ligand-based virtual screening, density functional theory, and dynamic simulation studies were employed to explore the identified compounds and co-crystallized molecule in the protein structure. From the diverse databases, we have identified several identical molecules based on their structural features, such as functional groups like hydrophobic (H), aromatic rings (R), hydrogen bond acceptor (A), and donor (D). The HHHPR five-point pharmacophore feature was identified as a template pharmacophore to search the potential compounds from the Enamine and LifeChemical databases and have a good fitness score with known renin inhibitors. Furthermore, theoretical validation was done through several studies that confirmed the activity of the identified molecules. Overall, we propose that these compounds might break the failure in adverse events and improve the potency of hypertension treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lakshmanan Loganathan
- Pharmacogenomics and CADD Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Jeyanthi Sankar
- Pharmacogenomics and CADD Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Kannan Rajendran
- Department of General Medicine, Saveetha Medical College and Hospital, Chennai, India
| | - Karthikeyan Muthusamy
- Pharmacogenomics and CADD Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
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20
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Dragomanova S, Andonova V, Volcho K, Salakhutdinov N, Kalfin R, Tancheva L. Therapeutic Potential of Myrtenal and Its Derivatives-A Review. Life (Basel) 2023; 13:2086. [PMID: 37895468 PMCID: PMC10608190 DOI: 10.3390/life13102086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/10/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
The investigation of monoterpenes as natural products has gained significant attention in the search for new pharmacological agents due to their ability to exhibit a wide range in biological activities, including antifungal, antibacterial, antioxidant, anticancer, antispasmodic, hypotensive, and vasodilating properties. In vitro and in vivo studies reveal their antidepressant, anxiolytic, and memory-enhancing effects in experimental dementia and Parkinson's disease. Chemical modification of natural substances by conjugation with various synthetic components is a modern method of obtaining new biologically active compounds. The discovery of new potential drugs among monoterpene derivatives is a progressive avenue within experimental pharmacology, offering a promising approach for the therapy of diverse pathological conditions. Biologically active substances such as monoterpenes, for example, borneol, camphor, geraniol, pinene, and thymol, are used to synthesize compounds with analgesic, anti-inflammatory, anticonvulsive, antidepressant, anti-Alzheimer's, antiparkinsonian, antiviral and antibacterial (antituberculosis) properties. Myrtenal is a perspective monoterpenoid with therapeutic potential in various fields of medicine. Its chemical modifications often lead to new or more pronounced biological effects. As an example, the conjugation of myrtenal with the established pharmacophore adamantane enables the augmentation of several of its pivotal properties. Myrtenal-adamantane derivatives exhibited a variety of beneficial characteristics, such as antimicrobial, antifungal, antiviral, anticancer, anxiolytic, and neuroprotective properties, which are worth examining in more detail and at length.
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Affiliation(s)
- Stela Dragomanova
- Department of Pharmacology, Toxicology and Pharmacotherapy, Faculty of Pharmacy, Medical University of Varna, 84 A Tsar Osvoboditel Blvd., 9002 Varna, Bulgaria;
| | - Velichka Andonova
- Department of Pharmaceutical Technologies, Faculty of Pharmacy, Medical University of Varna, 84 A Tsar Osvoboditel Blvd., 9002 Varna, Bulgaria;
| | - Konstantin Volcho
- Department of Medicinal Chemistry, Novosibirsk Institute of Organic Chemistry of the Russian Academy of Sciences, 9 Lavrentiev Av., 630090 Novosibirsk, Russia; (K.V.); (N.S.)
| | - Nariman Salakhutdinov
- Department of Medicinal Chemistry, Novosibirsk Institute of Organic Chemistry of the Russian Academy of Sciences, 9 Lavrentiev Av., 630090 Novosibirsk, Russia; (K.V.); (N.S.)
| | - Reni Kalfin
- Institute of Neurobiology, Bulgarian Academy of Sciences, Acad. G. Bonchev St., Block 23, 1113 Sofia, Bulgaria;
- Department of Healthcare, South-West University, 66 Ivan Mihailov St., 2700 Blagoevgrad, Bulgaria
| | - Lyubka Tancheva
- Institute of Neurobiology, Bulgarian Academy of Sciences, Acad. G. Bonchev St., Block 23, 1113 Sofia, Bulgaria;
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21
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Parveen S, Batool A, Shafiq N, Rashid M, Sultan A, Wondmie GF, Bin Jardan YA, Brogi S, Bourhia M. Developmental landscape of computational techniques to explore the potential phytochemicals from Punica granatum peels for their antioxidant activity in Alzheimer's disease. Front Mol Biosci 2023; 10:1252178. [PMID: 37886033 PMCID: PMC10598865 DOI: 10.3389/fmolb.2023.1252178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/21/2023] [Indexed: 10/28/2023] Open
Abstract
Alzheimer's disease (AD) is more commonly found in women than in men as the risk increases with age. Phytochemicals are screened in silico from Punica granatum peels for their antioxidant activity to be utilized for Alzheimer's disease. Alzheimer's disease is inhibited by the hormone estrogen, which protects the brain from the bad effects of amyloid beta and acetylcholine (ACh), and is important for memory processing. For the purpose, a library of about 1,000 compounds from P. granatum were prepared and studied by applying integrated computational calculations like 3D-QSAR, molecular docking, MD simulation, ADMET, and density functional theory (DFT). The 3D-QSAR model screened the active compounds B25, B29, B35, B40, B45, B46, B48, B61, and B66 by the field points and activity atlas model from the prepared library. At the molecular level, docking was performed on active compounds for leading hit compounds such as B25 and B35 that displayed a high MolDock score, efficacy, and compatibility with drug delivery against the antioxidant activity. Optimization of the structure and chemical reactivity parameter of the hit compound was calculated by DFT. Moreover, ADMET prediction was evaluated to check the bioavailability and toxicity of the hit compound. Hesperidin (B25) is found to be a hit compound after the whole study and can be synthesized for potent drug discovery in the future.
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Affiliation(s)
- Shagufta Parveen
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalababd, Pakistan
| | - Aneeqa Batool
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalababd, Pakistan
| | - Nusrat Shafiq
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalababd, Pakistan
| | - Maryam Rashid
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalababd, Pakistan
| | - Ayesha Sultan
- Department of Chemistry, University of Education, Lahore, Pakistan
| | | | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Simone Brogi
- Department of Pharmacy, Pisa University, Pisa, Italy
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
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22
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Chahbaoui N, Khamouli S, Alaqarbeh M, Belaidi S, Sinha L, Chtita S, Bouachrine M. Identification of novel curcumin derivatives against pancreatic cancer: a comprehensive approach integrating 3D-QSAR pharmacophore modeling, virtual screening, and molecular dynamics simulations. J Biomol Struct Dyn 2023:1-19. [PMID: 37811784 DOI: 10.1080/07391102.2023.2266502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/27/2023] [Indexed: 10/10/2023]
Abstract
Pancreatic cancer, known as the "silent killer," poses a daunting challenge in cancer therapy. The dysregulation of the PI3Kα signaling pathway in pancreatic cancer has attracted considerable interest as a promising target for therapeutic intervention. In this regard, the use of curcumin derivatives as inhibitors of PI3Kα has emerged, providing a novel and promising avenue for developing effective treatments for this devastating disease. Computational approaches were employed to explore this potential and investigate 58 curcumin derivatives with cytotoxic activity against the Panc-1 cell line. Our approach involved ligand-based pharmacophore modeling and atom-based 3D-QSAR analysis. The resulting QSAR model derived from the best-fitted pharmacophore hypothesis (AAHRR_1) demonstrated remarkable performance with high correlation coefficients (R2) of 0.990 for the training set and 0.977 for the test set. The cross-validation coefficient (Q2) of 0.971 also validated the model's predictive power. Tropsha's recommended criteria, including the Y-randomization test, were employed to ensure its reliability. Furthermore, an enrichment study was conducted to evaluate the model's performance in identifying active compounds. AAHRR_1 was used to screen a curated PubChem database of curcumin-related compounds. Two molecules (CID156189304 and CID154728220) exhibited promising pharmacokinetic properties and higher docking scores than Alpelisib, warranting further investigation. Extensive molecular dynamics simulations provided crucial insights into the conformational dynamics within the binding site, validating their stability and behavior. These findings contribute to our understanding of the potential therapeutic effectiveness of these compounds as PI3Kα inhibitors in pancreatic cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Narimene Chahbaoui
- Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Saida Khamouli
- Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Marwa Alaqarbeh
- Basic Science Department, Prince Al Hussein Bin Abdullah II Academy for Civil Protection, Al-Balqa Applied University, Al-Salt, Jordan
| | - Salah Belaidi
- Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Leena Sinha
- Physics Department, University of Lucknow, Lucknow, India
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
- Superior School of Technology - Khenifra (EST-Khenifra), University of Sultan Moulay Sliman, Khenifra, Morocco
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23
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Sharma A, Kumar R, Varadwaj P. Developing human olfactory network and exploring olfactory receptor-odorant interaction. J Biomol Struct Dyn 2023; 41:8941-8960. [PMID: 36310099 DOI: 10.1080/07391102.2022.2138976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
The Olfactory receptor (OR)-odorant interactions are perplexed. ORs can bind to structurally diverse odorants associated with one or more odor percepts. Various attempts have been made to understand the intricacies of OR-odorant interaction. In this study, experimentally documented OR-odorant interactions are investigated comprehensively to; (a) suggest potential odor percepts for ORs based on the OR-OR network; (b) determine how odorants interacting with specific ORs differ in terms of inherent pharmacophoric features and molecular properties, (c) identify molecular interactions that explained OR-odorant interactions of selective ORs; and (d) predict the probable role of ORs other than olfaction. Human olfactory receptor network (hORnet) is developed to study possible odor percepts for ORs. We identified six molecular properties which showed variation and significant patterns to differentiate odorants binding with five ORs. The pharmacophore analysis revealed that odorants subset of five ORs follow similar pharmacophore hypothesis, (one hydrogen acceptor and two hydrophobic regions) but differ in terms of distance and orientation of pharmacophoric features. To ascertain the binding site residues and key interactions between the selected ORs and their interacting odorants, 3D-structure modelling, docking and molecular dynamics studies were carried out. Lastly, the potential role of ORs beyond olfaction is explored. A human OR-OR network was developed to suggest possible odor percepts for ORs using empirically proven OR-odorant interactions. We sought to find out significant characteristics, molecular properties, and molecular interactions that could explain OR-odorant interactions and add to the understanding of the complex issue of odor perception.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anju Sharma
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, Uttar Pradesh, India
| | - Pritish Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
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24
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Ezati M, Ahmadi A, Behmard E, Najafi A. Identification of novel metallo-β-lactamases inhibitors using ligand-based pharmacophore modelling and structure-based virtual screening. J Biomol Struct Dyn 2023:1-16. [PMID: 37732367 DOI: 10.1080/07391102.2023.2258406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/06/2023] [Indexed: 09/22/2023]
Abstract
Metallo-β-lactamases (MBLs) are a group of enzymes that hydrolyze the most commonly used β-lactam-based antibiotics, leading to the development of multi-drug resistance. The three main clinically relevant groups of these enzymes are IMP, VIM, and NDM. This study aims to introduce potent novel overlapped candidates from a ZINC database retrieved from the 200,583-member natural library against the active sites of IMP-1, VIM-2, and NDM-1 through a straightforward computational workflow using virtual screening approaches. The screening pipeline started by assessing Lipinski's rule of five (RO5), drug-likeness, and pan-assay interference compounds (PAINS) which were used to generate a pharmacophore model using D-captopril as a standard inhibitor. The process was followed by the consensus docking protocol and molecular dynamic (MD) simulation combined with the molecular mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method to compute the total binding free energy and evaluate the binding characteristics. The absorption, distribution, metabolism, elimination, and toxicity (ADMET) profiles of the compounds were also analyzed, and the search space decreased to the final two inhibitory candidates for B1 subclass MBLs, which fulfilled all criteria for further experimental evaluation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Ezati
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Esmaeil Behmard
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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25
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Durgam L, Pagag J, Indra Neela Y, Guruprasad L. Mutational analyses, pharmacophore-based inhibitor design and in silico validation for Zika virus NS3-helicase. J Biomol Struct Dyn 2023:1-19. [PMID: 37712848 DOI: 10.1080/07391102.2023.2252929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
Zika virus is responsible for causing Zika infections and was declared as a public health emergency of international concern in February 2016. The Zika virus NS3-helicase is a viable drug target for the design of inhibitors due to its essential role in the replication of viral genome. The viral RNA is unwound by the NS3-helicase in order to enable the reproduction of viral genome by the NS5 protein. Zika virus infections in humans are being reported for the last 15 years. We have therefore carried out amino acid mutational analyses of NS3-helicase. NS3-helicase has two crucial binding sites: the ATP and RNA binding sites. The cofactor-ATP based pharmacophore was generated for virtual screening of ZINC database using Pharmit server, that is followed by molecular docking and molecular dynamics simulations of potential hits as probable Zika virus NS3-helicase inhibitors at the cofactor binding site. The drug-like properties of the molecules were analysed and, DFT calculations were performed on the five best molecules to reveal their stability in solvent phase compared to gas phase, the HOMO and LUMO and electrostatic potential maps to analyze the electronic and geometric characteristics. These are significant findings towards the discovery of new inhibitors of Zika virus NS3-helicase, a promising drug target to treat the Zika virus infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Laxman Durgam
- School of Chemistry, University of Hyderabad, Hyderabad, India
| | - Jishu Pagag
- School of Chemistry, University of Hyderabad, Hyderabad, India
| | - Y Indra Neela
- School of Chemistry, University of Hyderabad, Hyderabad, India
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26
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Kant R, Jha P, Saluja D, Chopra M. Identification of novel inhibitors of Neisseria gonorrhoeae MurI using homology modeling, structure-based pharmacophore, molecular docking, and molecular dynamics simulation-based approach. J Biomol Struct Dyn 2023; 41:7433-7446. [PMID: 36106953 DOI: 10.1080/07391102.2022.2121943] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
Abstract
MurI is one of the most significant role players in the biosynthesis of the peptidoglycan layer in Neisseria gonorrhoeae (Ng). We attempted to highlight the structural and functional relationship between Ng-MurI and D-glutamate to design novel molecules targeting this interaction. The three-dimensional (3D) model of the protein was constructed by homology modeling and the quality and consistency of generated model were assessed. The binding site of the protein was identified by molecular docking studies and a pharmacophore was identified using the interactions of the control ligand. The structure-based pharmacophore model was validated and employed for high-throughput virtual screening and molecular docking to identify novel Ng-MurI inhibitors. Finally, the model was optimized by molecular dynamics (MD) simulations and the optimized model complex with the substrate glutamate and novel molecules facilitated us to confirm the stability of the protein-ligand docked complexes. The 100 ns MD simulations of the potential lead compounds with protein confirmed that the modeled complexes were stable. This study identifies novel potential compounds with good fitness and docking scores, which made the interactions of biological significance within the protein active site. Hence, the identified compounds may act as new leads to design and develop Ng-MurI inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Kant
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research & Delhi School of Public Health, IoE, University of Delhi, Delhi, India
| | - Prakash Jha
- Laboratory of Molecular Modeling and Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Daman Saluja
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research & Delhi School of Public Health, IoE, University of Delhi, Delhi, India
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
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27
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Sar S, Mitra S, Panda P, Mandal SC, Ghosh N, Halder AK, Cordeiro MNDS. In Silico Modeling and Structural Analysis of Soluble Epoxide Hydrolase Inhibitors for Enhanced Therapeutic Design. Molecules 2023; 28:6379. [PMID: 37687207 PMCID: PMC10490281 DOI: 10.3390/molecules28176379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/17/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Human soluble epoxide hydrolase (sEH), a dual-functioning homodimeric enzyme with hydrolase and phosphatase activities, is known for its pivotal role in the hydrolysis of epoxyeicosatrienoic acids. Inhibitors targeting sEH have shown promising potential in the treatment of various life-threatening diseases. In this study, we employed a range of in silico modeling approaches to investigate a diverse dataset of structurally distinct sEH inhibitors. Our primary aim was to develop predictive and validated models while gaining insights into the structural requirements necessary for achieving higher inhibitory potential. To accomplish this, we initially calculated molecular descriptors using nine different descriptor-calculating tools, coupled with stochastic and non-stochastic feature selection strategies, to identify the most statistically significant linear 2D-QSAR model. The resulting model highlighted the critical roles played by topological characteristics, 2D pharmacophore features, and specific physicochemical properties in enhancing inhibitory potential. In addition to conventional 2D-QSAR modeling, we implemented the Transformer-CNN methodology to develop QSAR models, enabling us to obtain structural interpretations based on the Layer-wise Relevance Propagation (LRP) algorithm. Moreover, a comprehensive 3D-QSAR analysis provided additional insights into the structural requirements of these compounds as potent sEH inhibitors. To validate the findings from the QSAR modeling studies, we performed molecular dynamics (MD) simulations using selected compounds from the dataset. The simulation results offered crucial insights into receptor-ligand interactions, supporting the predictions obtained from the QSAR models. Collectively, our work serves as an essential guideline for the rational design of novel sEH inhibitors with enhanced therapeutic potential. Importantly, all the in silico studies were performed using open-access tools to ensure reproducibility and accessibility.
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Affiliation(s)
- Shuvam Sar
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India; (S.S.)
| | - Soumya Mitra
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India; (S.S.)
- Dr. B. C. Roy College of Pharmacy and Allied Health Sciences, Campus Dr. Meghnad Saha Sarani, Durgapur 713206, India
| | - Parthasarathi Panda
- Dr. B. C. Roy College of Pharmacy and Allied Health Sciences, Campus Dr. Meghnad Saha Sarani, Durgapur 713206, India
| | - Subhash C. Mandal
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India; (S.S.)
| | - Nilanjan Ghosh
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India; (S.S.)
| | - Amit Kumar Halder
- Dr. B. C. Roy College of Pharmacy and Allied Health Sciences, Campus Dr. Meghnad Saha Sarani, Durgapur 713206, India
- LAQV@REQUIMTE—Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Maria Natalia D. S. Cordeiro
- LAQV@REQUIMTE—Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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28
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Vennila KN, Elango KP. Insilico molecular modelling to identify PDK-1 targeting agents based on its protein-protein docking interaction. J Biomol Struct Dyn 2023:1-12. [PMID: 37646644 DOI: 10.1080/07391102.2023.2252080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023]
Abstract
PDK1, an attractive cancer target that downstreams 23 other kinases towards cell growth, survival and metabolism has gaining attention due to allosteric effect of ligands bound to it. Generally, the drug design strategy using pharmacophores is either a single protein structure or ensemble or ligand-based. Apart from these methods, yet another new approach of protein-protein docking with state of art computational tool like Schrodinger Suite to generate pharmacophores based on the interacting partners of the protein is proposed in this work. The structure-based pharmacophoric features were picked up from docking the ten interacting partners of PDK1 and screened against the Enamine libraries containing protein-protein interacting compound collection, advanced, protein mimetic and allosteric compounds. High throughput virtual screening against the PIF pocket of PDK1 yields an indole scaffold. The identified indole derivative is proposed to be a strong activator that binds in the protein-protein interaction site of PDK1 which was further confirmed by molecular metadynamics simulations, free energy surface analysis and MM-GBSA calculations. Thus, the pharmacophores generated by the interacting proteins for PPI can facilitate the virtual screening in structure-based drug discovery of similar therapeutic targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kailasam N Vennila
- The Gandhigram Rural Institute-Deemed to be University, Gandhigram, Tamil Nadu, India
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29
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Sharma V, Kaushik R, Kumar K, Gupta A, Srivastava S, Kurmi RK. Advancement in Epilepsy Pharmacotherapy: An Insight into the Pharmacophoric Approaches of Recent Drugs. Cent Nerv Syst Agents Med Chem 2023; 23:CNSAMC-EPUB-133922. [PMID: 37608651 DOI: 10.2174/1871524923666230822104733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/15/2023] [Accepted: 07/14/2023] [Indexed: 08/24/2023]
Abstract
Epilepsy is the most general, extensive, and severe neurological disorder, affecting more than 50 million individuals globally. Initially, conventional medicines and simple salts like potassium bromide were employed as antiepileptic medication candidates. Nowadays, many anticonvulsant drugs have been discovered as first-generation and second-generation and newer drugs and are still in development phases. The pharmacophore-based drug design process includes pharmacophore modeling and validation, pharmacophore-based virtual screening, virtual hits profiling, and lead identification with special reference. This comprehensive article reviews recently developed anticonvulsant derivatives on the basis of pharmacophoric approaches. A literature survey was performed using various search engines like Google Scholar, Scopus, Sci Finder, ScienceDirect, Science gate, Scilit, PubMed, NINDS database of NIH, Bentham Sciences, and other online and print journals and scientific databases. The presented review discusses such kinds of newer drugs that are in the market as well as in clinical trial phases. Detailed outcomes of pharmacophoric modeling have been discussed for newly derived derivatives like targets involved in Epilepsy, lead molecules etc., for the treatment of epilepsy. This exhaustive review will assist the researchers in the further development of potential antiepileptic agents.
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Affiliation(s)
- Vikas Sharma
- School of Pharmacy, Sharda University, Plot No. 32-34, K.P.- III, Greater Noida, Uttar Pradesh-201306, India
| | - Rahul Kaushik
- Metro College of Health Sciences and Research, , K.P.- III, Greater Noida, Uttar Pradesh-201306, India
| | - Krishan Kumar
- Metro College of Health Sciences and Research, , K.P.- III, Greater Noida, Uttar Pradesh-201306, India
| | - Akanksha Gupta
- United Institute of Pharmacy, Naini, Prayagraj (Allahabad), Uttar Pradesh, India
| | - Snigdha Srivastava
- Ram-Eesh Institute of Vocational and Technical Education. Plot No. 3, K.P.-1, Greater Noida, Uttar Pradesh-201306, India
| | - Rajan Kumar Kurmi
- Ram-Eesh Institute of Vocational and Technical Education. Plot No. 3, K.P.-1, Greater Noida, Uttar Pradesh-201306, India
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30
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Gratteri C, Ambrosio FA, Lupia A, Moraca F, Catalanotti B, Costa G, Bellocchi M, Carioti L, Salpini R, Ceccherini-Silberstein F, Frazia SL, Malagnino V, Sarmati L, Svicher V, Bryant S, Artese A, Alcaro S. Molecular and Structural Aspects of Clinically Relevant Mutations of SARS-CoV-2 RNA-Dependent RNA Polymerase in Remdesivir-Treated Patients. Pharmaceuticals (Basel) 2023; 16:1143. [PMID: 37631058 PMCID: PMC10459223 DOI: 10.3390/ph16081143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
(1) Background: SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is a promising therapeutic target to fight COVID-19, and many RdRp inhibitors nucleotide/nucleoside analogs, such as remdesivir, have been identified or are in clinical studies. However, the appearance of resistant mutations could reduce their efficacy. In the present work, we structurally evaluated the impact of RdRp mutations found at baseline in 39 patients treated with remdesivir and associated with a different degree of antiviral response in vivo. (2) Methods: A refined bioinformatics approach was applied to assign SARS-CoV-2 clade and lineage, and to define RdRp mutational profiles. In line with such a method, the same mutations were built and analyzed by combining docking and thermodynamics evaluations with both molecular dynamics and representative pharmacophore models. (3) Results: Clinical studies revealed that patients bearing the most prevalent triple mutant P323L+671S+M899I, which was present in 41% of patients, or the more complex mutational profile P323L+G671S+L838I+D738Y+K91E, which was found with a prevalence of 2.6%, showed a delayed reduced response to remdesivir, as confirmed by the increase in SARS-CoV-2 viral load and by a reduced theoretical binding affinity versus RdRp (ΔGbindWT = -122.70 kcal/mol; ΔGbindP323L+671S+M899I = -84.78 kcal/mol; ΔGbindP323L+G671S+L838I+D738Y+K91E = -96.74 kcal/mol). Combined computational approaches helped to rationalize such clinical observations, offering a mechanistic understanding of the allosteric effects of mutants on the global motions of the viral RNA synthesis machine and in the changes of the interactions patterns of remdesivir during its binding.
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Affiliation(s)
- Carmen Gratteri
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
| | - Francesca Alessandra Ambrosio
- Dipartimento di Medicina Sperimentale e Clinica, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy;
| | - Antonio Lupia
- Dipartimento di Scienze della vita e dell’ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy;
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Federica Moraca
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Bruno Catalanotti
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Maria Bellocchi
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Luca Carioti
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Romina Salpini
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Francesca Ceccherini-Silberstein
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Simone La Frazia
- Dipartimento di Biologia, Università Tor Vergata di Roma, Via della Ricerca Scientifica, 1, 00133 Roma, Italy; (S.L.F.); (V.S.)
| | - Vincenzo Malagnino
- Dipartimento di Medicina dei Sistemi, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (V.M.); (L.S.)
| | - Loredana Sarmati
- Dipartimento di Medicina dei Sistemi, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (V.M.); (L.S.)
| | - Valentina Svicher
- Dipartimento di Biologia, Università Tor Vergata di Roma, Via della Ricerca Scientifica, 1, 00133 Roma, Italy; (S.L.F.); (V.S.)
| | - Sharon Bryant
- Inte:Ligand GmbH, Mariahilferstrasse 74B/11, 1070 Vienna, Austria;
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
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Zhu J, Li X, Meng H, Jia L, Xu L, Cai Y, Chen Y, Jin J, Yu L, Gao M. Molecular modeling strategy for detailing the primary mechanism of action of copanlisib to PI3K: combined ligand-based and target-based approach. J Biomol Struct Dyn 2023:1-12. [PMID: 37572326 DOI: 10.1080/07391102.2023.2246569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/27/2023] [Indexed: 08/14/2023]
Abstract
Since dysregulation of the phosphatidylinositol 3-kinase (PI3K) signaling pathway is associated with the pathogenesis of cancer, inflammation, and autoimmunity, PI3K has emerged as an attractive target for drug development. Although copanlisib is the first pan-PI3K inhibitor to be approved for clinical use, the precise mechanism by which it acts on PI3K has not been fully elucidated. To reveal the binding mechanisms and structure-activity relationship between PI3K and copanlisib, a comprehensive modeling approach that combines 3D-quantitative structure-activity relationship (3D-QSAR), pharmacophore model, and molecular dynamics (MD) simulation was utilized. Initially, the structure-activity relationship of copanlisib and its derivatives were explored by constructing a 3D-QSAR. Then, the key chemical characteristics were identified by building common feature pharmacophore models. Finally, MD simulations were performed to elucidate the important interactions between copanlisib and different PI3K subtypes, and highlight the key residues for tight-binding inhibitors. The present study uncovered the principal mechanism of copanlisib's action on PI3K at the theoretical level, and these findings might provide guidance for the rational design of pan-PI3K inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jingyu Zhu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Xintong Li
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Huiqin Meng
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Lei Jia
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Yanfei Cai
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Yun Chen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Jian Jin
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Li Yu
- School of Inspection and Testing Certification, Changzhou Vocational Institute of Engineering, Changzhou, China
| | - Mingzhu Gao
- Department of Clinical Research Center for Jiangnan University Medical Center (Wuxi No.2 People's Hospital), Wuxi, China
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Zuo L, Huang S, He Y, Zhang L, Cheng G, Feng Y, Han Q, Ge L, Feng L. Design, Synthesis, and Bioassay for the Thiadiazole-Bridged Thioacetamide Compound as Cy-FBP/SBPase Inhibitors Based on Catalytic Mechanism Virtual Screening. J Agric Food Chem 2023; 71:11834-11846. [PMID: 37498729 DOI: 10.1021/acs.jafc.3c01913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphosphatase (Cy-FBP/SBPase) was an important regulatory enzyme in cyanobacterial photosynthesis and was a potential target enzyme for screening to obtain novel inhibitors against cyanobacterial blooms. In this study, we developed a novel pharmacophore screening model based on the catalytic mechanism and substrate structure of Cy-FBP/SBPase and screened 26 S series compounds with different structures and pharmacophore characteristics from the Specs database by computer-assisted drug screening. These compounds exhibited moderate inhibitory activity against Cy-FBP/SBPase, with 9 compounds inhibiting >50% at 100 μM. Among them, compound S5 showed excellent inhibitory activity against both Cy-FBP/SBPase and Synechocystis sp. PCC6803 (IC50 = 6.7 ± 0.7 μM and EC50 = 7.7 ± 1.4 μM). The binding mode of compound S5 to Cy-FBP/SBPase was predicted using the molecular docking theory and validated by sentinel mutation and enzyme activity analysis. Physiochemical, gene transcription level, and metabolomic analyses showed that compound S5 significantly reduced the quantum yield of photosystem II and the maximum electron transfer rate, downregulated transcript levels of related genes encoding the Calvin cycle and photosystem, reduced the photosynthetic efficiency of cyanobacteria, thus inhibited metabolic pathways, such as the Calvin cycle and tricarboxylic acid cycle, and eventually achieved an efficient algicide. In addition, compound S5 had a high safety profile for human-derived cells and zebrafish. In summary, the novel pharmacophore screening model obtained from the current work provides an effective solution to the cyanobacterial bloom problem.
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Affiliation(s)
- Lingzi Zuo
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University (CCNU), Wuhan, Hubei 430079, People's Republic of China
| | - Shi Huang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University (CCNU), Wuhan, Hubei 430079, People's Republic of China
| | - Yanlin He
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University (CCNU), Wuhan, Hubei 430079, People's Republic of China
| | - Liexiong Zhang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University (CCNU), Wuhan, Hubei 430079, People's Republic of China
| | - Guonian Cheng
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University (CCNU), Wuhan, Hubei 430079, People's Republic of China
| | - Yu Feng
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University (CCNU), Wuhan, Hubei 430079, People's Republic of China
| | - Qiang Han
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University (CCNU), Wuhan, Hubei 430079, People's Republic of China
| | - Li Ge
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University (CCNU), Wuhan, Hubei 430079, People's Republic of China
| | - Lingling Feng
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University (CCNU), Wuhan, Hubei 430079, People's Republic of China
- Wuhan Institute of Photochemistry and Technology, 7 North Bingang Road, Wuhan, Hubei 430083, People's Republic of China
- National Key Laboratory of Green Pesticide, Central China Normal University (CCNU), Wuhan, Hubei 430079, People's Republic of China
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Onikanni SA, Lawal B, Munyembaraga V, Bakare OS, Taher M, Khotib J, Susanti D, Oyinloye BE, Noriega L, Famuti A, Fadaka AO, Ajiboye BO. Profiling the Antidiabetic Potential of Compounds Identified from Fractionated Extracts of Entada africana toward Glucokinase Stimulation: Computational Insight. Molecules 2023; 28:5752. [PMID: 37570723 PMCID: PMC10420681 DOI: 10.3390/molecules28155752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/05/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Glucokinase plays an important role in regulating the blood glucose level and serves as an essential therapeutic target in type 2 diabetes management. Entada africana is a medicinal plant and highly rich source of bioactive ligands with the potency to develop new target drugs for glucokinase such as diabetes and obesity. Therefore, the study explored a computational approach to predict identified compounds from Entada africana following its intermolecular interactions with the allosteric binding site of the enzymes. We retrieved the three-dimensional (3D) crystal structure of glucokinase (PDB ID: 4L3Q) from the online protein data bank and prepared it using the Maestro 13.5, Schrödinger Suite 2022-3. The compounds identified were subjected to ADME, docking analysis, pharmacophore modeling, and molecular simulation. The results show the binding potential of the identified ligands to the amino acid residues, thereby suggesting an interaction of the amino acids with the ligand at the binding site of the glucokinase activator through conventional chemical bonds such as hydrogen bonds and hydrophobic interactions. The compatibility of the molecules was highly observed when compared with the standard ligand, thereby leading to structural and functional changes. Therefore, the bioactive components from Entada africana could be a good driver of glucokinase, thereby paving the way for the discovery of therapeutic drugs for the treatment of diabetes and its related complications.
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Affiliation(s)
- Sunday Amos Onikanni
- College of Medicine, Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan;
- Department of Chemical Sciences, Biochemistry Unit, Afe-Babalola University, Ado-Ekiti 360101, Ekiti State, Nigeria;
| | - Bashir Lawal
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, USA;
| | - Valens Munyembaraga
- Institute of Translational Medicine and New Drug Development, College of Medicine, China Medical University, Taichung 40402, Taiwan;
- University Teaching Hospital of Butare, Huye 15232, Rwanda
| | - Oluwafemi Shittu Bakare
- Department of Biochemistry, Faculty Science, Adekunle Ajasin University, Akungba Akoko 342111, Ondo State, Nigeria;
| | - Muhammad Taher
- Department of Pharmaceutical Technology, Kulliyyah of Pharmacy, International Islamic University Malaysia, Kuantan 25200, Pahang, Malaysia;
- Pharmaceutics and Translational Research Group, Kulliyyah of Pharmacy, International Islamic University Malaysia, Kuantan 25200, Pahang, Malaysia
| | - Junaidi Khotib
- Department of Pharmacy Practice, Faculty of Pharmacy, Airlangga University, Surabaya 60115, Indonesia
| | - Deny Susanti
- Department of Chemistry, Kulliyyah of Science, International Islamic University Malaysia, Kuantan 25200, Pahang, Malaysia;
| | - Babatunji Emmanuel Oyinloye
- Department of Chemical Sciences, Biochemistry Unit, Afe-Babalola University, Ado-Ekiti 360101, Ekiti State, Nigeria;
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
- Institute of Drug Research and Development, SE Bogoro Center, Afe Babalola University, PMB 5454, Ado-Ekiti 360001, Ekiti State, Nigeria;
| | - Lloyd Noriega
- College of Medicine, Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan;
| | - Ayodeji Famuti
- Honey T Scientific Company, Ibadan 234002, Oyo State, Nigeria;
| | | | - Basiru Olaitan Ajiboye
- Institute of Drug Research and Development, SE Bogoro Center, Afe Babalola University, PMB 5454, Ado-Ekiti 360001, Ekiti State, Nigeria;
- Phytomedicine and Molecular Toxicology Research Laboratory, Department of Biochemistry, Federal University, Oye-Ekiti 371104, Ekiti State, Nigeria
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Shin SH, Ye MK, Chae MH, Geum SY, Aboraia AS, Abdel-Aal ABM, Qayed WS, Abd El-wahab HAA, Abou-Ghadir OF, Aboul-Fadl T. Effects of Lidocaine-Derived Organic Compounds on Eosinophil Activation and Survival. Molecules 2023; 28:5696. [PMID: 37570665 PMCID: PMC10420271 DOI: 10.3390/molecules28155696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Lidocaine, a local anesthetic, is known to possess anti-inflammatory properties. However, its clinical use is limited by inconveniences, such as its local synesthetic effects. This study evaluated lidocaine analogs designed and synthesized to overcome the disadvantages of lidocaine, having anti-inflammatory properties. Interleukin 5 (IL-5)-induced eosinophil activation and survival were evaluated using 36 lidocaine analogs with modified lidocaine structure on the aromatic or the acyl moiety or both. Eosinophil survival was evaluated using a CellTiter 96® aqueous cell proliferation assay kit. Superoxide production was determined using the superoxide dismutase-inhibitable reduction of cytochrome C method. Eosinophil cationic protein (ECP), IL-8, and transcription factor expression were determined using enzyme-linked immunosorbent assay. The platelet-activating factor (PAF)-induced migration assay was performed using a Transwell insert system. Compounds EI137 and EI341 inhibited IL-5-induced eosinophil survival and superoxide and ECP production in a concentration-dependent manner. These compounds also significantly reduced IL-8 production. Although compounds EI137 and EI341 significantly reduced phosphorylated ERK 1/2 expression, they did not influence other total and phosphorylated transcription factors. Moreover, 1000 µM of compound EI341 only inhibited PAF-induced migration of eosinophils. Lidocaine analogs EI137 and EI341 inhibited IL-5-mediated activation and survival of eosinophils. These compounds could be new therapeutic agents to treat eosinophilic inflammatory diseases.
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Affiliation(s)
- Seung-Heon Shin
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea; (M.-K.Y.); (M.-H.C.); (S.-Y.G.)
| | - Mi-Kyung Ye
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea; (M.-K.Y.); (M.-H.C.); (S.-Y.G.)
| | - Mi-Hyun Chae
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea; (M.-K.Y.); (M.-H.C.); (S.-Y.G.)
| | - Sang-Yen Geum
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea; (M.-K.Y.); (M.-H.C.); (S.-Y.G.)
| | - Ahmed S. Aboraia
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt; (A.S.A.); (W.S.Q.); (H.A.A.A.E.-w.); (T.A.-F.)
| | - Abu-Baker M. Abdel-Aal
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt; (A.-B.M.A.-A.); (O.F.A.-G.)
| | - Wesam S. Qayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt; (A.S.A.); (W.S.Q.); (H.A.A.A.E.-w.); (T.A.-F.)
| | - Hend A. A. Abd El-wahab
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt; (A.S.A.); (W.S.Q.); (H.A.A.A.E.-w.); (T.A.-F.)
| | - Ola F. Abou-Ghadir
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt; (A.-B.M.A.-A.); (O.F.A.-G.)
| | - Tarek Aboul-Fadl
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt; (A.S.A.); (W.S.Q.); (H.A.A.A.E.-w.); (T.A.-F.)
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Sukumaran S, Prasanna VM, Panicker LK, Nair AS, Oommen OV. Discovery of a new Daboia russelli viper venom PLA 2 inhibitor using virtual screening of pharmacophoric features of co-crystallized compound. J Biomol Struct Dyn 2023:1-14. [PMID: 37490072 DOI: 10.1080/07391102.2023.2238072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Snake venom PLA2, a member of the group of hydrolase enzymes, has been recognized as a promising drug target for snake envenomation. In the present study, an attempt was made to identify potential inhibitors of snake venom PLA2 by employing a pharmacophore-based virtual screening, docking, and dynamics approach. A receptor-based pharmacophore model was generated based on the features of the established and bound co-crystal ligand (2-carbamoylmethyl-5-propyl-octahydro-indol-7-yl)-acetic acid in the PLA2 complex. The best pharmacophore model (ADDH) derived, consisted of four features, namely one hydrogen bond acceptor, two hydrogen bond donors, and one hydrophobic region. This common pharmacophore was then used to perform virtual screening against a drug-like diverse database, with due consideration to the Lipinski 'rule of five', so as to obtain a pool of lead molecules. The short-listed lead molecules were then subjected to docking analysis with that of the Daboia russelli viper venom PLA2 followed by a molecular simulation study for a duration of 100 ns. CAP04815700 was chosen as the best compound based on the simulation parameters, which were then taken for MM/PBSA calculation, and it was revealed that it has a similar effective inhibitory potential as that of the crystal ligand. Further, the cluster analysis also revealed the structural significance of the backbone protein after the interaction with CAP04815700. This study will continue to explore its bioactivity in vitro and in vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suveena Sukumaran
- Centre for venom informatics, Department of Computational Biology and Bioinformatics, University of Kerala, Trivandrum, Kerala, India
- Department of Computational Biology & Bioinformatics, University of Kerala, Trivandrum, Kerala, India
| | - Vinod Manoharan Prasanna
- Centre for venom informatics, Department of Computational Biology and Bioinformatics, University of Kerala, Trivandrum, Kerala, India
| | - Laladhas Krishna Panicker
- Centre for venom informatics, Department of Computational Biology and Bioinformatics, University of Kerala, Trivandrum, Kerala, India
- Department of Computational Biology & Bioinformatics, University of Kerala, Trivandrum, Kerala, India
| | - Achuthsankar S Nair
- Centre for venom informatics, Department of Computational Biology and Bioinformatics, University of Kerala, Trivandrum, Kerala, India
| | - Oommen V Oommen
- Centre for venom informatics, Department of Computational Biology and Bioinformatics, University of Kerala, Trivandrum, Kerala, India
- Department of Computational Biology & Bioinformatics, University of Kerala, Trivandrum, Kerala, India
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Patinote C, Raevens S, Baumann A, Pellegrin E, Bonnet PA, Deleuze-Masquéfa C. [1,2,4]triazolo[4,3- a]quinoxaline as Novel Scaffold in the Imiqualines Family: Candidates with Cytotoxic Activities on Melanoma Cell Lines. Molecules 2023; 28:5478. [PMID: 37513350 PMCID: PMC10384284 DOI: 10.3390/molecules28145478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
Cutaneous melanoma is one of the most aggressive human cancers and is the deadliest form of skin cancer, essentially due to metastases. Novel therapies are always required, since cutaneous melanoma develop resistance to oncogenic pathway inhibition treatment. The Imiqualine family is composed of heterocycles diversely substituted around imidazo[1,2-a]quinoxaline, imidazo[1,2-a]pyrazine, imidazo[1,5-a]quinoxaline, and pyrazolo[1,5-a]quinoxaline scaffolds, which display interesting activities on a panel of cancer cell lines, especially melanoma cell lines. We have designed and prepared novel compounds based on the [1,2,4]triazolo[4,3-a]quinoxaline scaffold through a common synthetic route, using 1-chloro-2-hydrazinoquinoxaline and an appropriate aldehyde. Cyclization is ensured by an oxidation-reduction mechanism using chloranil. The substituents on positions 1 and 8 were chosen based on previous structure-activity relationship (SAR) studies conducted within our heterocyclic Imiqualine family. Physicochemical parameters of all compounds have also been predicted. A375 melanoma cell line viability has been evaluated for 16 compounds. Among them, three novel [1,2,4]triazolo[4,3-a]quinoxalines display cytotoxic activities. Compounds 16a and 16b demonstrate relative activities in the micromolar range (respectively, 3158 nM and 3527 nM). Compound 17a shows the best EC50 of the novel series (365 nM), even if EAPB02303 remains the lead of the entire Imiqualine family (3 nM).
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Affiliation(s)
- Cindy Patinote
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 F16, (CNRS, ENSCM, Université de Montpellier), 1919 Route de Mende, 34090 Montpellier, France
| | - Sandy Raevens
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 F16, (CNRS, ENSCM, Université de Montpellier), 1919 Route de Mende, 34090 Montpellier, France
| | - Amélie Baumann
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 F16, (CNRS, ENSCM, Université de Montpellier), 1919 Route de Mende, 34090 Montpellier, France
| | - Eloise Pellegrin
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 F16, (CNRS, ENSCM, Université de Montpellier), 1919 Route de Mende, 34090 Montpellier, France
| | - Pierre-Antoine Bonnet
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 F16, (CNRS, ENSCM, Université de Montpellier), 1919 Route de Mende, 34090 Montpellier, France
| | - Carine Deleuze-Masquéfa
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 F16, (CNRS, ENSCM, Université de Montpellier), 1919 Route de Mende, 34090 Montpellier, France
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37
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Chan LC, Lee HK, Wang L, Chaili S, Xiong YQ, Bayer AS, Proctor RA, Yeaman MR. Diflunisal and Analogue Pharmacophores Mediating Suppression of Virulence Phenotypes in Staphylococcus aureus. Antibiotics (Basel) 2023; 12:1180. [PMID: 37508276 PMCID: PMC10376238 DOI: 10.3390/antibiotics12071180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/26/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Invasive methicillin-resistant Staphylococcus aureus (MRSA) infections are leading causes of morbidity and mortality that are complicated by increasing resistance to conventional antibiotics. Thus, minimizing virulence and enhancing antibiotic efficacy against MRSA is a public health imperative. We originally demonstrated that diflunisal (DIF; [2-hydroxy-5-(2,4-difluorophenyl) benzoic acid]) inhibits S. aureus virulence factor expression. To investigate pharmacophores that are active in this function, we evaluated a library of structural analogues for their efficacy to modulate virulence phenotypes in a panel of clinically relevant S. aureus isolates in vitro. Overall, the positions of the phenyl, hydroxyl, and carboxylic moieties and the presence or type of halogen (F vs. Cl) influenced the efficacy of compounds in suppressing hemolysis, proteolysis, and biofilm virulence phenotypes. Analogues lacking halogens inhibited proteolysis to an extent similar to DIF but were ineffective at reducing hemolysis or biofilm production. In contrast, most analogues lacking the hydroxyl or carboxylic acid groups did not suppress proteolysis but did mitigate hemolysis and biofilm production to an extent similar to DIF. Interestingly, chirality and the substitution of fluorine with chlorine resulted in a differential reduction in virulence phenotypes. Together, this pattern of data suggests virulence-suppressing pharmacophores of DIF and structural analogues integrate halogen, hydroxyl, and carboxylic acid moiety stereochemistry. The anti-virulence effects of DIF were achieved using concentrations that are safe in humans, do not impair platelet antimicrobial functions, do not affect S. aureus growth, and do not alter the efficacy of conventional antibiotics. These results offer proof of concept for using novel anti-virulence strategies as adjuvants to antibiotic therapy to address the challenge of MRSA infection.
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Affiliation(s)
- Liana C Chan
- Division of Molecular Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Division of Infectious Diseases, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
- Institute for Infection and Immunity, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Hong K Lee
- Division of Molecular Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Institute for Infection and Immunity, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Ling Wang
- Division of Molecular Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Institute for Infection and Immunity, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Siyang Chaili
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, 2311 Pierce Ave., Nashville, TN 37232, USA
| | - Yan Q Xiong
- Division of Infectious Diseases, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
- Institute for Infection and Immunity, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Arnold S Bayer
- Division of Infectious Diseases, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
- Institute for Infection and Immunity, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Richard A Proctor
- Departments of Medical Microbiology & Immunology and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Michael R Yeaman
- Division of Molecular Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Division of Infectious Diseases, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
- Institute for Infection and Immunity, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
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Primavera E, Palazzotti D, Barreca ML, Astolfi A. Computer-Aided Identification of Kinase-Targeted Small Molecules for Cancer: A Review on AKT Protein. Pharmaceuticals (Basel) 2023; 16:993. [PMID: 37513905 PMCID: PMC10384952 DOI: 10.3390/ph16070993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
AKT (also known as PKB) is a serine/threonine kinase that plays a pivotal regulatory role in the PI3K/AKT/mTOR signaling pathway. Dysregulation of AKT activity, especially its hyperactivation, is closely associated with the development of various human cancers and resistance to chemotherapy. Over the years, a wide array of AKT inhibitors has been discovered through experimental and computational approaches. In this regard, herein we present a comprehensive overview of AKT inhibitors identified using computer-assisted drug design methodologies (including docking-based and pharmacophore-based virtual screening, machine learning, and quantitative structure-activity relationships) and successfully validated small molecules endowed with anticancer activity. Thus, this review provides valuable insights to support scientists focused on AKT inhibition for cancer treatment and suggests untapped directions for future computer-aided drug discovery efforts.
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Affiliation(s)
- Erika Primavera
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, 06123 Perugia, Italy
| | - Deborah Palazzotti
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, 06123 Perugia, Italy
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, 06123 Perugia, Italy
| | - Andrea Astolfi
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, 06123 Perugia, Italy
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Bülbül EF, Robaa D, Sun P, Mahmoudi F, Melesina J, Zessin M, Schutkowski M, Sippl W. Application of Ligand- and Structure-Based Prediction Models for the Design of Alkylhydrazide-Based HDAC3 Inhibitors as Novel Anti-Cancer Compounds. Pharmaceuticals (Basel) 2023; 16:968. [PMID: 37513880 PMCID: PMC10386743 DOI: 10.3390/ph16070968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Histone deacetylases (HDAC) represent promising epigenetic targets for several diseases including different cancer types. The HDAC inhibitors approved to date are pan-HDAC inhibitors and most show a poor selectivity profile, side effects, and in particular hydroxamic-acid-based inhibitors lack good pharmacokinetic profiles. Therefore, the development of isoform-selective non-hydroxamic acid HDAC inhibitors is a highly regarded field in medicinal chemistry. In this study, we analyzed different ligand-based and structure-based drug design techniques to predict the binding mode and inhibitory activity of recently developed alkylhydrazide HDAC inhibitors. Alkylhydrazides have recently attracted more attention as they have shown promising effects in various cancer cell lines. In this work, pharmacophore models and atom-based quantitative structure-activity relationship (QSAR) models were generated and evaluated. The binding mode of the studied compounds was determined using molecular docking as well as molecular dynamics simulations and compared with known crystal structures. Calculated free energies of binding were also considered to generate QSAR models. The created models show a good explanation of in vitro data and were used to develop novel HDAC3 inhibitors.
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Affiliation(s)
- Emre F Bülbül
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Dina Robaa
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Ping Sun
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Fereshteh Mahmoudi
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jelena Melesina
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Matthes Zessin
- Department of Enzymology, Institute of Biotechnology, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biotechnology, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
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Zandona A, Madunić J, Miš K, Maraković N, Dubois-Geoffroy P, Cavaco M, Mišetić P, Padovan J, Castanho M, Jean L, Renard PY, Pirkmajer S, Neves V, Katalinić M. Biological response and cell death signaling pathways modulated by tetrahydroisoquinoline-based aldoximes in human cells. Toxicology 2023:153588. [PMID: 37419273 DOI: 10.1016/j.tox.2023.153588] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
The uncharged 3-hydroxy-2-pyridine aldoximes with protonatable tertiary amines are studied as antidotes in toxic organophosphates (OP) poisoning. Due to some of their specific structural features, we hypothesize that these compounds could exert diverse biological activity beyond their main scope of application. To examine this further, we performed an extensive cell-based assessment to determine their effects on human cells (SH-SY5Y, HEK293, HepG2, HK-2, myoblasts and myotubes) and possible mechanism of action. As our results indicated, aldoxime having a piperidine moiety did not induce significant toxicity up to 300µM within 24hours, while those with a tetrahydroisoquinoline moiety, in the same concentration range, showed time-dependent effects and stimulated mitochondria-mediated activation of the intrinsic apoptosis pathway through ERK1/2 and p38-MAPK signaling and subsequent activation of initiator caspase 9 and executive caspase 3 accompanied with DNA damage as observed already after 4hour exposure. Mitochondria and fatty acid metabolism were also likely targets of 3-hydroxy-2-pyridine aldoximes with tetrahydroisoquinoline moiety, due to increased phosphorylation of acetyl-CoA carboxylase. In silico analysis predicted kinases as their most probable target class, while pharmacophores modeling additionally predicted the inhibition of a cytochrome P450cam. Overall, if the absence of significant toxicity for piperidine bearing aldoxime highlights the potential of its further studies in medical counter-measures, the observed biological activity of aldoximes with tetrahydroisoquinoline moiety could be indicative for future design of compounds either in a negative context in OP antidotes design, or in a positive one for design of compounds for the treatment of other phenomena like cell proliferating malignancies.
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Affiliation(s)
- Antonio Zandona
- Institute for Medical Research and Occupational Health, POB 291, HR-10001 Zagreb, Croatia.
| | - Josip Madunić
- Institute for Medical Research and Occupational Health, POB 291, HR-10001 Zagreb, Croatia.
| | - Katarina Miš
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | - Nikola Maraković
- Institute for Medical Research and Occupational Health, POB 291, HR-10001 Zagreb, Croatia.
| | | | - Marco Cavaco
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
| | | | | | - Miguel Castanho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
| | - Ludovic Jean
- Université Paris Cité, CNRS, INSERM, CiTCoM (UMR 8038), F-75006, Paris, France.
| | - Pierre-Yves Renard
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), 76000 Rouen, France.
| | - Sergej Pirkmajer
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | - Vera Neves
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
| | - Maja Katalinić
- Institute for Medical Research and Occupational Health, POB 291, HR-10001 Zagreb, Croatia.
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Siddiqui AJ, Badraoui R, Jahan S, Alshahrani MM, Siddiqui MA, Khan A, Adnan M. Targeting NMDA receptor in Alzheimer's disease: identifying novel inhibitors using computational approaches. Front Pharmacol 2023; 14:1208968. [PMID: 37416066 PMCID: PMC10319995 DOI: 10.3389/fphar.2023.1208968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023] Open
Abstract
The glutamate-gated ion channels known as N-methyl-d-aspartate receptors (NMDARs) are important for both normal and pathological brain function. Subunit-selective antagonists have high therapeutic promise since many pathological conditions involve NMDAR over activation, although few clinical successes have been reported. Allosteric inhibitors of GluN2B-containing receptors are among the most potential NMDAR targeting drugs. Since the discovery of ifenprodil, a variety of GluN2B-selective compounds have been discovered, each with remarkably unique structural motifs. These results expand the allosteric and pharmacolog-ical spectrum of NMDARs and provide a new structural basis for the development of next-generation GluN2B antagonists that have therapeutic potential in brain diseases. Small molecule therapeutic inhibitors targeting NMDA have recently been developed to target CNS disorders such as Alzheimer's disease. In the current study, a cheminformatics method was used to discover potential antagonists and to identify the structural requirements for Gly/NMDA antagonism. In this case we have created a useful pharmacophore model with solid statistical values. Through pharmacophore mapping, the verified model was used to filter out virtual matches from the ZINC database. Assessing receptor-ligand binding mechanisms and affinities used molecular docking. To find the best hits, the GlideScore and the interaction of molecules with important amino acids were considered essential features. We found some molecular inhibitors, namely, ZINC13729211, ZINC07430424, ZINC08614951, ZINC60927204, ZINC12447511, and ZINC18889258 with high binding affinity using computational methods. The molecules in our studies showed characteristics such as good stability, hydrogen bonding and higher binding affinities in the solvation-based assessment method than ifenprodil with acceptable ADMET profile. Moreover, these six leads have been proposed as potential new perspectives for exploring potent Gly/NMDA receptor antagonists. In addition, it can be tested in the laboratory for potential therapeutic strategies for both in vitro and in vivo research.
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Affiliation(s)
- Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | - Riadh Badraoui
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | - Sadaf Jahan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | | | - Andleeb Khan
- Department of Pharmacology and Toxicology, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
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Lotfi B, Mebarka O, Khan SU, Htar TT. Pharmacophore-based virtual screening, molecular docking and molecular dynamics studies for the discovery of novel neuraminidase inhibitors. J Biomol Struct Dyn 2023:1-13. [PMID: 37334701 DOI: 10.1080/07391102.2023.2225007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The in silico evaluation of 27 p-aminosalicylic acid derivatives, also referred to as neuraminidase inhibitors was the focus of the current study. To search and predict new potential neuraminidase inhibitors, this study was based on the ligand-based pharmacophore modeling, 3D QSAR, molecular docking, ADMET and MD simulation studies. The data was generated from recently reported inhibitors and divided into two groups, one of these group has 17 compounds for training and the second group has 10 compounds for testing purpose. The generated pharmacophore has known as ADDPR_4 was found statistically significant 3D-QSAR model owing the high trust scores (R2 = 0.974, Q2 = 0.905, RMSE = 0.23). Morever external validation was also employed to evaluate the prediction capacity of the built pharmacophore model (R2pred = 0.905). In addition, in silico ADMET, analyses were employed to evaluate the obtained hits for drug likeness properties. The stability of formed complexes was further evaluated using molecular dynamics. Top two hits showed stable complexes with Neuraminidase based on calculated total binding energy by MM-PBSA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bourougaa Lotfi
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Ouassaf Mebarka
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Shafi Ullah Khan
- Product and Process Innovation Department, Qarshi Brands Pvt. Ltd. Hattar Industrial Estate, Haripur, KPK, Pakistan
| | - Thet Thet Htar
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Selangor, Malaysia
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Ejaz SA, Aziz M, Fawzy Ramadan M, Fayyaz A, Bilal MS. Pharmacophore-Based Virtual Screening and In-Silico Explorations of Biomolecules (Curcumin Derivatives) of Curcuma longa as Potential Lead Inhibitors of ERBB and VEGFR-2 for the Treatment of Colorectal Cancer. Molecules 2023; 28:molecules28104044. [PMID: 37241785 DOI: 10.3390/molecules28104044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 05/28/2023] Open
Abstract
The newly FDA-approved drug, Axitinib, is an effective therapy against RTKs, but it possesses severe adverse effects like hypertension, stomatitis, and dose-dependent toxicity. In order to ameliorate Axitinib's downsides, the current study is expedited to search for energetically stable and optimized pharmacophore features of 14 curcumin (1,7-bis(4-hydroxy-3-methoxyphenyl)hepta-1,6-diene-3,5-dione) derivatives. The rationale behind the selection of curcumin derivatives is their reported anti-angiogenic and anti-cancer properties. Furthermore, they possessed a low molecular weight and a low toxicity profile. In the current investigation, the pharmacophore model-based drug design, facilitates the filtering of curcumin derivatives as VEGFR2 interfacial inhibitors. Initially, the Axitinib scaffold was used to build a pharmacophore query model against which curcumin derivatives were screened. Then, top hits from pharmacophore virtual screening were subjected to in-depth computational studies such as molecular docking, density functional theory (DFT) studies, molecular dynamics (MD) simulations, and ADMET property prediction. The findings of the current investigation revealed the substantial chemical reactivity of the compounds. Specifically, compounds S8, S11, and S14 produced potential molecular interactions against all four selected protein kinases. Docking scores of -41.48 and -29.88 kJ/mol for compounds S8 against VEGFR1 and VEGFR3, respectively, were excellent. Whereas compounds S11 and S14 demonstrated the highest inhibitory potential against ERBB and VEGFR2, with docking scores of -37.92 and -38.5 kJ/mol against ERBB and -41.2 and -46.5 kJ/mol against VEGFR-2, respectively. The results of the molecular docking studies were further correlated with the molecular dynamics simulation studies. Moreover, HYDE energy was calculated through SeeSAR analysis, and the safety profile of the compounds was predicted through ADME studies.
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Affiliation(s)
- Syeda Abida Ejaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Mubashir Aziz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Mohamed Fawzy Ramadan
- Department of Clinical Nutrition, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ammara Fayyaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Muhammad Sajjad Bilal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
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Anjum NF, Shanmugarajan D, Prashantha Kumar BR, Faizan S, Durai P, Raju RM, Javid S, Purohit MN. Novel Derivatives of Eugenol as a New Class of PPARγ Agonists in Treating Inflammation: Design, Synthesis, SAR Analysis and In Vitro Anti-Inflammatory Activity. Molecules 2023; 28:molecules28093899. [PMID: 37175309 PMCID: PMC10180488 DOI: 10.3390/molecules28093899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 05/15/2023] Open
Abstract
The main objective of this research was to develop novel compounds from readily accessed natural products especially eugenol with potential biological activity. Eugenol, the principal chemical constituent of clove (Eugenia caryophyllata) from the family Myrtaceae is renowned for its pharmacological properties, which include analgesic, antidiabetic, antioxidant, anticancer, and anti-inflammatory effects. According to reports, PPARγ regulates inflammatory reactions. The synthesized compounds were structurally analyzed using FT-IR, 1HNMR, 13CNMR, and mass spectroscopy techniques. Molecular docking was performed to analyze binding free energy and important amino acids involved in the interaction between synthesized derivatives and the target protein. The development of the structure-activity relationship is based on computational studies. Additionally, the stability of the best-docked protein-ligand complexes was assessed using molecular dynamic modeling. The in-vitro PPARγ competitive binding Lanthascreen TR-FRET assay was used to confirm the affinity of compounds to the target protein. All the synthesized derivatives were evaluated for an in vitro anti-inflammatory activity using an albumin denaturation assay and HRBC membrane stabilization at varying concentrations from 6.25 to 400 µM. In this background, with the aid of computational research, we were able to design six novel derivatives of eugenol synthesized, analyzed, and utilized TR-FRET competitive binding assay to screen them for their ability to bind PPARγ. Anti-inflammatory activity evaluation through in vitro albumin denaturation and HRBC method revealed that 1f exhibits maximum inhibition of heat-induced albumin denaturation at 50% and 85% protection against HRBC lysis at 200 and 400 µM, respectively. Overall, we found novel derivatives of eugenol that could potentially reduce inflammation by PPARγ agonism.
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Affiliation(s)
- Noor Fathima Anjum
- Department of Pharmaceutical Chemistry, Farooqia College of Pharmacy, Mysuru 570 015, India
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570 015, India
| | - Dhivya Shanmugarajan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570 015, India
| | - B R Prashantha Kumar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570 015, India
| | - Syed Faizan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570 015, India
| | - Priya Durai
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570 015, India
| | - Ruby Mariam Raju
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570 015, India
| | - Saleem Javid
- Department of Pharmaceutical Chemistry, Farooqia College of Pharmacy, Mysuru 570 015, India
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570 015, India
| | - Madhusudan N Purohit
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570 015, India
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Chuanxi Y, Xiaoning W, Chang G, Yunxiang L, Ziyi M, Jinqiu Z, Haoce W, Lin L, Yonglin L, Haofen S, Weiliang W. Molecular Mechanism and Structure-activity Relationship of the Inhibition Effect between Monoamine Oxidase and Selegiline Analogues. Curr Comput Aided Drug Des 2023:CAD-EPUB-131440. [PMID: 37138424 DOI: 10.2174/1573409919666230503143055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/19/2023] [Accepted: 03/27/2023] [Indexed: 05/05/2023]
Abstract
INTRODUCTION To investigate the inhibition properties and structure-activity relationship between monoamine oxidase (MAO) and selected monoamine oxidase inhibitors (MAOIs, including selegiline, rasagiline and clorgiline). METHODS The inhibition effect and molecular mechanism between MAO and MAOIs were identified via the half maximal inhibitory concentration (IC50) and molecular docking technology. RESULTS It was indicated that selegiline and rasagiline were MAO B inhibitors, but clorgiline was MAO-A inhibitor based on the selectivity index (SI) of MAOIs (0.000264, 0.0197 and 14607.143 for selegiline, rasagiline and clorgiline, respectively). The high-frequency amino acid residues of the MAOIs and MAO were Ser24, Arg51, Tyr69 and Tyr407 for MAO-A and Arg42 and Tyr435 for MAO B. The MAOIs and MAO A/B pharmacophores included the aromatic core, hydrogen bond acceptor, hydrogen bond donor-acceptor and hydrophobic core. CONCLUSION This study shows the inhibition effect and molecular mechanism between MAO and MAOIs and provides valuable findings on the design and treatment of Alzheimer's and Parkinson's diseases.
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Affiliation(s)
- Yang Chuanxi
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, Shandong, 266520, China
| | - Wang Xiaoning
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang, Liaoning, 110819, China
| | - Gao Chang
- Qingdao Jiaming Measurement and Control Technology Co., Ltd., Qingdao, Shandong, 266000, China
| | - Liu Yunxiang
- Environmental Monitoring Station of Yuncheng County Environmental Protection Bureau, Heze, Shandong, 274700, China
| | - Ma Ziyi
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, Shandong, 266520, China
| | - Zang Jinqiu
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, Shandong, 266520, China
| | - Wang Haoce
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, Shandong, 266520, China
| | - Liu Lin
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, Shandong, 266520, China
| | - Liu Yonglin
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, Shandong, 266520, China
| | - Sun Haofen
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, Shandong, 266520, China
| | - Wang Weiliang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, Shandong, 266520, China
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Roy A, Luharuka S, Paul I, Ray S. Design and development of novel potential inhibitors of the human USP21 enzyme using a pharmacophore-based virtual screening technique. J Mol Recognit 2023:e3023. [PMID: 37096811 DOI: 10.1002/jmr.3023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 03/13/2023] [Accepted: 04/19/2023] [Indexed: 04/26/2023]
Abstract
An overexpression and increase have been observed in the concentration and activity of the USP21 enzyme in many cancers, necessitating the need for the development of new inhibitor drugs against the same. The current study attempts to discover one such novel potential inhibitor of USP21 by the application of various bioinformatics techniques which include molecular modelling, pharmacophore mapping, and pharmacophore-based virtual screening, molecular docking, and ADMET prediction followed by molecular dynamics simulations. Following this inverted-funnel-like approach, we finally ended up with one ligand- ZINC02422616 which displays a very high binding affinity towards the USP21 domain. This ligand contains all the pharmacophoric features displayed by the compounds that are potential inhibitors of the USP21 domain. Moreover, it shows a favourable pharmacokinetic, pharmacodynamic, and ADMET profile along with strong hydrophobic interaction and hydrogen bonding with the domain. Simulation studies showed that the complex remains stable over time, with the bound protein displaying a more constrained motion in the conformational space compared to the unbound form. The ligand showed a highly favourable free energy landscape/surface, forming several energy minimas in contrast to the unbound domain in which most conformations occupied a relatively higher energy state. Moreover, the ligand also displayed a Kd of 422.8nM and a free energy of binding ΔG of -8.6kcal/mol, both of which indicate a very high affinity towards the target domain.This potential drug candidate can then be used as a viable treatment method for many types of cancers caused by USP21. his article is protected by copyright. All rights reserved.
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Affiliation(s)
- Alankar Roy
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Shreya Luharuka
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Ishani Paul
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India
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Bieri C, Esmel A, Keita M, Owono LCO, Dali B, Megnassan E, Miertus S, Frecer V. Structure-Based Design and Pharmacophore-Based Virtual Screening of Combinatorial Library of Triclosan Analogues Active against Enoyl-Acyl Carrier Protein Reductase of Plasmodium falciparum with Favourable ADME Profiles. Int J Mol Sci 2023; 24:ijms24086916. [PMID: 37108083 PMCID: PMC10139228 DOI: 10.3390/ijms24086916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Cost-effective therapy of neglected and tropical diseases such as malaria requires everlasting drug discovery efforts due to the rapidly emerging drug resistance of the plasmodium parasite. We have carried out computational design of new inhibitors of the enoyl-acyl carrier protein reductase (ENR) of Plasmodium falciparum (PfENR) using computer-aided combinatorial and pharmacophore-based molecular design. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) complexation QSAR model was developed for triclosan-based inhibitors (TCL) and a significant correlation was established between the calculated relative Gibbs free energies of complex formation (∆∆Gcom) between PfENR and TCL and the observed inhibitory potencies of the enzyme (IC50exp) for a training set of 20 known TCL analogues. Validation of the predictive power of the MM-PBSA QSAR model was carried out with the generation of 3D QSAR pharmacophore (PH4). We obtained a reasonable correlation between the relative Gibbs free energy of complex formation ∆∆Gcom and IC50exp values, which explained approximately 95% of the PfENR inhibition data: pIC50exp=-0.0544×∆∆Gcom+6.9336,R2=0.95. A similar agreement was established for the PH4 pharmacophore model of the PfENR inhibition (pIC50exp=0.9754×pIC50pre+0.1596, R2=0.98). Analysis of enzyme-inhibitor binding site interactions suggested suitable building blocks to be used in a virtual combinatorial library of 33,480 TCL analogues. Structural information derived from the complexation model and the PH4 pharmacophore guided us through in silico screening of the virtual combinatorial library of TCL analogues to finally identify potential new TCL inhibitors effective at low nanomolar concentrations. Virtual screening of the library by PfENR-PH4 led to a predicted IC50pre value for the best inhibitor candidate as low as 1.9 nM. Finally, the stability of PfENR-TCLx complexes and the flexibility of the active conformation of the inhibitor for selected top-ranking TCL analogues were checked with the help of molecular dynamics. This computational study resulted in a set of proposed new potent inhibitors with predicted antimalarial effects and favourable pharmacokinetic profiles that act on a novel pharmacological target, PfENR.
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Affiliation(s)
- Cecile Bieri
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
| | - Akori Esmel
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
| | - Melalie Keita
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
| | - Luc Calvin Owono Owono
- Department of Physics, Ecole Normale Supérieure, University of Yaoundé I, P.O. Box 47, Yaoundé 1, Cameroon
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia
| | - Brice Dali
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
| | - Eugene Megnassan
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia
- International Centre for Theoretical Physics, Strada Costiera 11, I-34151 Trieste, Italy
- Laboratoire de Cristallographie-Physique Moléculaire, Université De Cocody, Abidjan 22, Côte d'Ivoire
- Laboratoire de Chimie Organique Structurale et Théorique, Université De Cocody, Abidjan 22, Côte d'Ivoire
| | - Stanislav Miertus
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia
- Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia
| | - Vladimir Frecer
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, SK-83232 Bratislava, Slovakia
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Kumar Biswas S, Sasmal P, Koley A, Jana R, Biswas J. WITHDRAWN: Design and Discovery of Lophine Derivatives as Multitargeting Agents by Molecular Docking, ADMET, MD Simulation and Pharmacophore Analysis: A Computational Approach. Comb Chem High Throughput Screen 2023; 26:CCHTS-EPUB-130229. [PMID: 36959130 DOI: 10.2174/1386207326666230320103446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/02/2023] [Accepted: 02/13/2023] [Indexed: 03/25/2023]
Abstract
Since the authors are not responding to the editor’s requests to fulfill the editorial requirement, therefore, the article has been withdrawn from the journal "Combinatorial Chemistry & High Throughput Screening". Bentham Science apologizes to the readers of the journal for any inconvenience this may have caused. The Bentham Editorial Policy on Article Withdrawal can be found at https://benthamscience.com/editorial-policies-main.php BENTHAM SCIENCE DISCLAIMER It is a condition of publication that manuscripts submitted to this journal have not been published and will not be simultaneously submitted or published elsewhere. Furthermore, any data, illustration, structure or table that has been published elsewhere must be reported, and copyright permission for reproduction must be obtained. Plagiarism is strictly forbidden, and by submitting the article for publication the authors agree that the publishers have the legal right to take appropriate action against the authors, if plagiarism or fabricated information is discovered. By submitting a manuscript the authors agree that the copyright of their article is transferred to the publishers if and when the article is accepted for publication.
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Affiliation(s)
- Shyamal Kumar Biswas
- Department of Pharmaceutical Chemistry, Calcutta Institute of Pharmaceutical Technology & Allied Health Sciences, Uluberia, Howrah, West Bengal - 711 316, India
| | - Pujan Sasmal
- Department of Pharmaceutical Chemistry, Calcutta Institute of Pharmaceutical Technology & Allied Health Sciences, Uluberia, Howrah, West Bengal - 711 316, India
- Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka - 560 107, India
| | - Akash Koley
- Department of Pharmacology, Calcutta Institute of Pharmaceutical Technology & Allied Health Sciences, Uluberia, Howrah, West Bengal - 711 316, India
| | - Rimpa Jana
- Department of Pharmaceutical Chemistry, Calcutta Institute of Pharmaceutical Technology & Allied Health Sciences, Uluberia, Howrah, West Bengal - 711 316, India
- Department of Pharmaceutical Chemistry, Flemming College of Pharmacy, Baruipur, North 24 Parganas, West Bengal - 700 144, India
| | - Jagrity Biswas
- School of Health Sciences, The Neotia University, Diamond Harbour Road, South 24 Parganas, West Bengal - 743 368, India
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Samy CRA, Karunanithi K, Sheshadhri J, Rengarajan M, Srinivasan P, Cherian P. ( R)-(+)-Rosmarinic Acid as an Inhibitor of Herpes and Dengue Virus Replication: an In Silico Assessment. Rev Bras Farmacogn 2023; 33:543-550. [PMID: 37151219 PMCID: PMC9994773 DOI: 10.1007/s43450-023-00381-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/20/2023] [Indexed: 03/28/2023]
Abstract
Since ancient times, viruses such as dengue, herpes, Ebola, AIDS, influenza, chicken meat, and SARS have been roaming around causing great health burdens. Currently, the prescribed antiviral drugs have not cured the complications caused by viruses, whereas viral replication was not controlled by them. The treatments suggested are not only ineffectual, but also sometimes inefficient against viruses at all stages of the viral cycle as well. To fight against these contagious viruses, people rely heavily on medicinal plants to enhance their innate and adaptive immune systems. In this research, the preparation of ligands and proteins was performed using the Maestro V.13.2 module tool. This software, consisting of LigPrep, Grid Generation, SiteMap, and Glide XP, has each contributed significantly to the preparation of ligands and proteins. Ultimately, the research found that (R)-(+)-rosmarinic acid was found to have significant docking scores of − 10.847 for herpes virus, of − 10.033 for NS5, and − 7.259 for NS1. In addition, the Prediction of Activity Spectra for Substances (PASS) server indicates that rosmarinic acid possesses a diverse spectrum of enzymatic activities, as probability active (Pa) values start at > 0.751, whereas it has fewer adverse effects than the drugs prescribed for viruses. Accordingly, it was found the rate of acute toxicity values of (R)-(+)-rosmarinic acid at doses LD50 log10 (mmol/g) and LD50 (mg/g) in different routes of administration, such as intraperitoneal, intravenous, oral, and subcutaneous. Ultimately, the present study concluded that (R)-(+)-rosmarinic acid would expose significant antiviral effects in in vitro and in vivo experiments, and this research would be a valuable asset for the future, especially for those who wish to discover a drug molecule for a variety of viruses.
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Affiliation(s)
- Christy Rani Arokia Samy
- Department of Chemistry, Thiru. Vi. Ka. Government Arts College, Kidarankondan, Thiruvarur, Tamil Nadu India 610 003
| | - Kalaimathi Karunanithi
- Department of Chemistry, Government College of Engineering, Sengipatti, Thanjavur, Tamil Nadu India 613 402
| | - Jayasree Sheshadhri
- Department of Chemistry, Prince Shri Venkateshwara Padmavathy Engineering College, Ponmar, Chennai, 600 127 India
| | - Murugesan Rengarajan
- Department of Zoology, Annai Vailankanni Arts and Science College, Bishop Sundaram Campus, Thanjavur, Tamil Nadu 613 007 India
| | - Prabhu Srinivasan
- Department of Botany, Annai Vailankanni Arts and Science College, Bishop Sundaram Campus, Thanjavur, Tamil Nadu 613 007 India
| | - Pinkie Cherian
- Department of Botany, St Joseph’s College for Women, Alappuzha, Kerala 688 001 India
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50
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Ademuwagun IA, Oduselu GO, Rotimi SO, Adebiyi E. Pharmacophore-Aided Virtual Screening and Molecular Dynamics Simulation Identifies TrkB Agonists for Treatment of CDKL5-Deficiency Disorders. Bioinform Biol Insights 2023; 17:11779322231158254. [PMID: 36895324 PMCID: PMC9989394 DOI: 10.1177/11779322231158254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/31/2023] [Indexed: 03/06/2023] Open
Abstract
Therapeutic intervention in cyclin-dependent kinase-like 5 (CDKL5) deficiency disorders (CDDs) has remained a concern over the years. Recent advances into the mechanistic interplay of signalling pathways has revealed the role of deficient tropomyosin receptor kinase B (TrkB)/phospholipase C γ1 signalling cascade in CDD. Novel findings showed that in vivo administration of a TrkB agonist, 7,8-dihydroxyflavone (7,8-DHF), resulted in a remarkable reversal in the molecular pathologic mechanisms underlying CDD. Owing to this discovery, this study aimed to identify more potent TrkB agonists than 7,8-DHF that could serve as alternatives or combinatorial drugs towards effective management of CDD. Using pharmacophore modelling and multiple database screening, we identified 691 compounds with identical pharmacophore features with 7,8-DHF. Virtual screening of these ligands resulted in identification of at least 6 compounds with better binding affinities than 7,8-DHF. The in silico pharmacokinetic and ADMET studies of the compounds also indicated better drug-like qualities than those of 7,8-DHF. Postdocking analyses and molecular dynamics simulations of the best hits, 6-hydroxy-10-(2-oxo-1-azatricyclo[7.3.1.05,13]trideca-3,5(13),6,8-tetraen-3-yl)-8-oxa-13,14,16-triazatetracyclo[7.7.0.02,7.011,15]hexadeca-1,3,6,9,11,15-hexaen-5-one (PubChem: 91637738) and 6-hydroxy-10-(8-methyl-2-oxo-1H-quinolin-3-yl)-8-oxa-13,14,16-triazatetracyclo[7.7.0.02,7.011,15]hexadeca-1,3,6,9,11,15-hexaen-5-one (PubChem ID: 91641310), revealed unique ligand interactions, validating the docking findings. We hereby recommend experimental validation of the best hits in CDKL5 knock out models before consideration as drugs in CDD management.
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Affiliation(s)
- Ibitayo Abigail Ademuwagun
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
- Department of Biochemistry, Covenant University, Ota, Nigeria
| | - Gbolahan Oladipupo Oduselu
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
- Department of Chemistry, Covenant University, Ota, Nigeria
| | - Solomon Oladapo Rotimi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
- Department of Biochemistry, Covenant University, Ota, Nigeria
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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