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Naik S, Soumya V, Mamledesai SN, Manickavasagam M, Choudhari P, Rathod S. Discovery of Substituted 2-oxoquinolinylthiazolidin-4-one Analogues as Potential EGFRK Inhibitors in Lung Cancer Treatment. Drug Res (Stuttg) 2024; 74:227-240. [PMID: 38830371 DOI: 10.1055/a-2305-2789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
PURPOSE Cancer is the second leading cause of death globally and is responsible for an estimated 9.6 million deaths in 2018. Globally, about 1 in 6 deaths is due to cancer and the chemotherapeutic drugs available have high toxicity and have reported side effects hence, there is a need for the synthesis of novel drugs in the treatment of cancer. METHODS The current research work dealt with the synthesis of a series of 3-(3-acetyl-2-oxoquinolin-1-(2H)-yl-2-(substitutedphenyl)thiazolidin-4-one (Va-j) derivatives and evaluation of their in-vitro anticancer activity. All the synthesized compounds were satisfactorily characterized by IR and NMR data. Compounds were further evaluated for their in-vitro anticancer activity against A-549 (lung cancer) cell lines. The in-vitro anticancer activity was based upon the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide (MTT) assay method. RESULTS The synthesized compounds exhibited satisfactory anticancer properties against the A-549 cell line. The compound (VH): showed the highest potency amongst the tested derivatives against the A-549 cell line with IC50 values of 100 µg/ml respectively and was also found to be more potent than Imatinib (150 µg/ml) which was used as a standard drug. Molecular docking studies of the titled compounds (Va-j) were carried out using AutoDock Vina/PyRx software. The synthesized compounds exhibited well-conserved hydrogen bonds with one or more amino acid residues in the active pocket of the EGFRK tyrosine kinase domain (PDB 1m17). CONCLUSION Among all the synthesized analogues, the binding affinity of the compound (Vh) was found to be higher than other synthesized derivatives and a molecular dynamics simulation study explored the stability of the docked complex system.
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Affiliation(s)
- Soniya Naik
- Department of Pharmaceutical Chemistry, Sri Ramachandra Faculty of Pharmacy, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
- Department of Pharmaceutical Chemistry, P.E.S's Rajaram and Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, Goa, India
| | - Vasu Soumya
- Department of Pharmaceutical Chemistry, Sri Ramachandra Faculty of Pharmacy, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
| | - Shivlingrao N Mamledesai
- Department of Pharmaceutical Chemistry, P.E.S's Rajaram and Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, Goa, India
| | - M Manickavasagam
- Department of Oncology, SRMC & RI, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, Maharashtra, India
| | - Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, Maharashtra, India
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Lübbers J, Lessel U, Rarey M. Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. J Chem Inf Model 2024; 64:2008-2020. [PMID: 38466793 DOI: 10.1021/acs.jcim.4c00147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Chemical fragment spaces exceed traditional virtual compound libraries by orders of magnitude, making them ideal search spaces for drug design projects. However, due to their immense size, they are not compatible with traditional analysis and search algorithms that rely on the enumeration of molecules. In this paper, we present SpaceProp2, an evolution of the SpaceProp algorithm, which enables the calculation of exact property distributions for chemical fragment spaces without enumerating them. We extend the original algorithm by the capabilities to compute distributions for the TPSA, the number of rotatable bonds, and the occurrence of user-defined molecular structures in the form of SMARTS patterns. Furthermore, SpaceProp2 produces example molecules for every property bin, enabling a detailed interpretation of the distributions. We demonstrate SpaceProp2 on six established make-on-demand chemical fragment spaces as well as BICLAIM, the in-house fragment space of Boehringer Ingelheim. The possibility to search multiple SMARTS patterns simultaneously as well as the produced example molecules offers previously impossible insights into the composition of these vast combinatorial molecule collections, making it an ideal tool for the analysis and design of chemical fragment spaces.
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Affiliation(s)
- Justin Lübbers
- ZBH - Center for Bioinformatics, Research Group for Computational Molecular Design, Universität Hamburg, Hamburg 22761, Germany
| | - Uta Lessel
- Computational Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss 88437, Germany
| | - Matthias Rarey
- ZBH - Center for Bioinformatics, Research Group for Computational Molecular Design, Universität Hamburg, Hamburg 22761, Germany
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Blicharska N, Ben Ahmed Z, Jackson S, Rotondo D, Seidel V. In silico studies on the anti-acne potential of Garcinia mangostana xanthones and benzophenones. Z NATURFORSCH C 2024; 79:47-60. [PMID: 38549398 DOI: 10.1515/znc-2023-0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/09/2024] [Indexed: 05/01/2024]
Abstract
Garcinia mangostana fruits are used traditionally for inflammatory skin conditions, including acne. In this study, an in silico approach was employed to predict the interactions of G. mangostana xanthones and benzophenones with three proteins involved in the pathogenicity of acne, namely the human JNK1, Cutibacterium acnes KAS III and exo-β-1,4-mannosidase. Molecular docking analysis was performed using Autodock Vina. The highest docking scores and size-independent ligand efficiency values towards JNK1, C. acnes KAS III and exo-β-1,4-mannosidase were obtained for garcinoxanthone T, gentisein/2,4,6,3',5'-pentahydroxybenzophenone and mangostanaxanthone VI, respectively. To the best of our knowledge, this is the first report of the potential of xanthones and benzophenones to interact with C. acnes KAS III. Molecular dynamics simulations using GROMACS indicated that the JNK1-garcinoxanthone T complex had the highest stability of all ligand-protein complexes, with a high number of hydrogen bonds predicted to form between this ligand and its target. Petra/Osiris/Molinspiration (POM) analysis was also conducted to determine pharmacophore sites and predict the molecular properties of ligands influencing ADMET. All ligands, except for mangostanaxanthone VI, showed good membrane permeability. Garcinoxanthone T, gentisein and 2,4,6,3',5'-pentahydroxybenzophenone were identified as the most promising compounds to explore further, including in experimental studies, for their anti-acne potential.
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Affiliation(s)
- Natalia Blicharska
- Strathclyde Institute of Pharmacy & Biomedical Sciences, 3527 University of Strathclyde , Glasgow, UK
| | - Ziyad Ben Ahmed
- Laboratory of Fundamental Science, University Amar Telidji, Laghouat, Algeria
- Department of Analytical Chemistry, Applied Chemometrics and Molecular Modelling, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Simon Jackson
- Botanical Research Department, Davines S.p.A. Via Don Angelo Calzolari 55/A, Parma 43126, Italy
| | - Dino Rotondo
- Strathclyde Institute of Pharmacy & Biomedical Sciences, 3527 University of Strathclyde , Glasgow, UK
| | - Veronique Seidel
- Strathclyde Institute of Pharmacy & Biomedical Sciences, 3527 University of Strathclyde , Glasgow, UK
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Möbitz H. Design Principles for Balancing Lipophilicity and Permeability in beyond Rule of 5 Space. ChemMedChem 2024; 19:e202300395. [PMID: 37986275 DOI: 10.1002/cmdc.202300395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/13/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
An ab initio conformational analysis of oral beyond Rule of 5 (bRo5) drugs was complemented with measured permeability and logP(octanol) to derive design principles conferring oral bioavailability. 3D polar surface area (PSA) thresholds for oral bRo5 drugs coincided with those reported for Ro5 space. The majority of oral bRo5 drugs exceeded the Ro5 logP threshold of 5, reflecting a bias for permeability. Above 500 Da molecular weight (MW), oral drugs and highly permeable Novartis compounds occupy a narrow polarity range (topological or TPSA/MW) of 0.1-0.3 Å2 /Da, whose upper half coincides with the lower 90 percentiles of the Novartis logP set. This TPSA/MW range and 3D PSA below 100 Å2 define the "Rule of ~1 /₅" for balancing lipophilicity and permeability. Neutral TPSA, defined as TPSA minus 3D PSA occurs independent of conformation, intramolecular hydrogen bonds (IMHB) and MW, suggesting it is an intrinsic molecular property. Neutral TPSA increased in the lead optimization (LO) campaigns of three first in class de novo designed bRo5 drugs and may be a useful design parameter in bRo5 space.
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Affiliation(s)
- Henrik Möbitz
- Computer-Aided Drug Design, Global Discovery Chemistry, Novartis BioMedical Research, 4002, Basel, Switzerland
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Sang Z, Zhang T, Wang Z, De Clercq E, Pannecouque C, Kang D, Zhan P, Liu X. Design and synthesis of Fsp 3-enriched spirocyclic-substituted diarylpyrimidine derivatives as novel HIV-1 NNRTIs. Chem Biol Drug Des 2024; 103:e14510. [PMID: 38519265 DOI: 10.1111/cbdd.14510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/13/2024] [Accepted: 03/12/2024] [Indexed: 03/24/2024]
Abstract
In this study, a novel series of diarylpyrimidine derivatives with Fsp3-enriched spirocycles were designed and synthesized to further explore the chemical space of the hydrophobic channel of the NNRTI-binding pocket. The biological evaluation results showed that most of the compounds displayed effective inhibitory potency against the HIV-1 wild-type strain, with EC50 values ranging from micromolar to submicromolar levels. Among them, TT6 turned out to be the most effective inhibitor with an EC50 value of 0.17 μM, demonstrating up to 47 times more active than that of reference drug 3TC (EC50 = 8.01 μM). More encouragingly, TT6 was found to potently inhibit the HIV-1 mutant strain K103N with an EC50 value of 0.69 μM, being about 6-fold more potent than 3TC (EC50 = 3.68 μM) and NVP (EC50 = 4.62 μM). Furthermore, TT6 exhibited the most potent inhibitory activity toward HIV-1 reverse transcriptase with an IC50 value of 0.33 μM. Additionally, molecular simulation studies were conducted to investigate the binding modes between TT6 and NNRTI-binding pocket, which may provide valuable clues for the follow-up structural optimizations.
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Affiliation(s)
- Zihao Sang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Tao Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan, Shandong, China
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Leuven, Belgium
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan, Shandong, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan, Shandong, China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan, Shandong, China
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Bhattacharjee A, Chaulya NC, Mukhopadhyay G, Chakraborty A, Mondal B. Optimization of Self-Double Emulsifying Drug Delivery System Using Design of Experiments for Enhanced Oral Bioavailability of Gentamicin: In-vitro, Ex-vivo and In-vivo Studies. J Pharm Sci 2024; 113:659-668. [PMID: 37607594 DOI: 10.1016/j.xphs.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 08/24/2023]
Abstract
Water-in-oil-in-water (w/o/w) double emulsions have shown excellent capability in augmenting the enteral bioavailability of BCS class III drugs, besides being effective controlled-release formulations. However, the problem of thermodynamic instability has restrained their industrial applicability. The self-double emulsifying drug delivery system (SDEDDS) is one of several approaches used to improve the stability of double emulsions. SDEDDS is a mixture of primary emulsion and secondary surfactant that can spontaneously emulsify into double emulsions in an external aqueous environment with mild agitation. Here, we prepared SDEDDS of gentamicin sulfate by response surface methodology. Selected optimized formulations (ODS1 and ODS2) were evaluated for zeta potential (Y1), optical clarity (Y2), release at 420 min (Y3), emulsion stability index (Y4) and self-emulsification time (Y5). For ODS1, Y1=-35.45 (±1.06)mV, Y2=53.19 (±0.35)%, Y3=75.79 (±0.60)%, Y4=93.97(±0.15)% and Y5=0.631 (±0.014)min, whereas for ODS2, Y1=-35.70 (±0.56)mV, Y2=48.09 (±0.64)%, Y3=76.61 (±0.99)%, Y4=93.00(±0.94)% and Y5=0.687(±0.02)min. Furthermore, ex-vivo studies on intestinal permeability revealed that SDEDDS improved membrane permeability compared to drug solution. Histopathology investigations revealed that SDEDDS promoted permeation without causing significant local membrane distortion. In addition, in-vivo studies revealed a 2.84 -fold increase in AUC0-∞ of optimized SDEDD compared to pure drug oral solution.
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Affiliation(s)
- Arka Bhattacharjee
- Department of Pharmaceutical Technology, Maulana Abul Kalam Azad University of Technology, NH 12, Haringhata, West Bengal 741249, India.
| | - Nitai Chand Chaulya
- Department of Pharmaceutical Technology, Gupta College of Technological Sciences, Ashram More, G.T. Road, Asansol, West Bengal 713301, India
| | - Goutam Mukhopadhyay
- Department of Pharmaceutical Technology, BCDA College of pharmacy and Technology, Campus 2, Udairajpur, Madhyamgram, West Bengal 700129, India
| | - Arpan Chakraborty
- Department of Pharmaceutical Technology, Maulana Abul Kalam Azad University of Technology, NH 12, Haringhata, West Bengal 741249, India
| | - Baishakhi Mondal
- Department of Pharmaceutical Technology, Maulana Abul Kalam Azad University of Technology, NH 12, Haringhata, West Bengal 741249, India
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Sabt A, Khedr MA, Eldehna WM, Elshamy AI, Abdelhameed MF, Allam RM, Batran RZ. New pyrazolylindolin-2-one based coumarin derivatives as anti-melanoma agents: design, synthesis, dual BRAF V600E/VEGFR-2 inhibition, and computational studies. RSC Adv 2024; 14:5907-5925. [PMID: 38370458 PMCID: PMC10870110 DOI: 10.1039/d4ra00157e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Malignant melanoma is the most invasive skin cancer with the highest risk of death. The inhibition of BRAFV600E appears relevant for overcoming secondary resistance developed during melanoma treatment. BRAFV600E triggers angiogenesis via modification of the expression of angiogenic inducers, which play a crucial role in the metastasis of melanoma. Accordingly, the dual inhibition of the BRAFV600E/VEGFR-2 signaling pathway is considered a rational approach in the design of anti-melanoma candidates. In this study, a new class of pyrazolylindolin-2-one linked coumarin derivatives as dual BRAFV600E/VEGFR-2 inhibitors targeting A375 melanoma cells was designed. Target compounds were tailored to occupy the pockets of BRAFV600E and VEGFR-2. Most of the synthesized compounds demonstrated potent mean growth inhibitory activity against A375 cells. Compound 4j was the most active cytotoxic derivative, displaying an IC50 value at a low micromolar concentration of 0.96 μM with a significant safety profile. Moreover, 4j showed dual potent inhibitory activity against BRAFV600E and VEGFR-2 (IC50 = 1.033 and 0.64 μM, respectively) and was more active than the reference drug sorafenib. Furthermore, derivative 4j caused significant G0/G1 cell cycle arrest, induced apoptosis, and inhibited the migration of melanoma cells. Molecular docking showed that compound 4j achieved the highest ΔG value of -9.5 kcal mol-1 against BRAFV600E and significant ΔG of -8.47 kcal mol-1 against VEGFR-2. Furthermore, the structure-activity relationship study revealed that TPSA directly contributed to the anticancer activity of the tested compounds.
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Affiliation(s)
- Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre Dokki Cairo 12622 Egypt
| | - Mohammed A Khedr
- Department of Pharmaceutical Chemistry, College of Pharmacy, Kuwait University Safat 13110 Kuwait
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University 11795 Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University Kafrelsheikh 33516 Egypt
| | - Abdelsamed I Elshamy
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre Dokki Cairo 12622 Egypt
| | - Mohamed F Abdelhameed
- Pharmacology Department, Medical and Clinical Research Institute, National Research Centre Dokki Cairo 12622 Egypt
| | - Rasha M Allam
- Pharmacology Department, Medical and Clinical Research Institute, National Research Centre Dokki Cairo 12622 Egypt
| | - Rasha Z Batran
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre Dokki Cairo 12622 Egypt
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Aiman S, Farooq QUA, Han Z, Aslam M, Zhang J, Khan A, Ahmad A, Li C, Ali Y. Core-genome-mediated promising alternative drug and multi-epitope vaccine targets prioritization against infectious Clostridium difficile. PLoS One 2024; 19:e0293731. [PMID: 38241420 PMCID: PMC10798517 DOI: 10.1371/journal.pone.0293731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/18/2023] [Indexed: 01/21/2024] Open
Abstract
Prevention of Clostridium difficile infection is challenging worldwide owing to its high morbidity and mortality rates. C. difficile is currently being classified as an urgent threat by the CDC. Devising a new therapeutic strategy become indispensable against C. difficile infection due to its high rates of reinfection and increasing antimicrobial resistance. The current study is based on core proteome data of C. difficile to identify promising vaccine and drug candidates. Immunoinformatics and vaccinomics approaches were employed to construct multi-epitope-based chimeric vaccine constructs from top-ranked T- and B-cell epitopes. The efficacy of the designed vaccine was assessed by immunological analysis, immune receptor binding potential and immune simulation analyses. Additionally, subtractive proteomics and druggability analyses prioritized several promising and alternative drug targets against C. difficile. These include FMN-dependent nitroreductase which was prioritized for pharmacophore-based virtual screening of druggable molecule databases to predict potent inhibitors. A MolPort-001-785-965 druggable molecule was found to exhibit significant binding affinity with the conserved residues of FMN-dependent nitroreductase. The experimental validation of the therapeutic targets prioritized in the current study may worthy to identify new strategies to combat the drug-resistant C. difficile infection.
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Affiliation(s)
- Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Qurrat ul Ain Farooq
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Zhongjie Han
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Muneeba Aslam
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Jilong Zhang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Abbas Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, KP, Pakistan
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Yasir Ali
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, Hong Kong
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Ronaldson PT, Davis TP. Blood-brain barrier transporters: a translational consideration for CNS delivery of neurotherapeutics. Expert Opin Drug Deliv 2024; 21:71-89. [PMID: 38217410 PMCID: PMC10842757 DOI: 10.1080/17425247.2024.2306138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/12/2024] [Indexed: 01/15/2024]
Abstract
INTRODUCTION Successful neuropharmacology requires optimization of CNS drug delivery and, by extension, free drug concentrations at brain molecular targets. Detailed assessment of blood-brain barrier (BBB) physiological characteristics is necessary to achieve this goal. The 'next frontier' in CNS drug delivery is targeting BBB uptake transporters, an approach that requires evaluation of brain endothelial cell transport processes so that effective drug accumulation and improved therapeutic efficacy can occur. AREAS COVERED BBB permeability of drugs is governed by tight junction protein complexes (i.e., physical barrier) and transporters/enzymes (i.e., biochemical barrier). For most therapeutics, a component of blood-to-brain transport involves passive transcellular diffusion. Small molecule drugs that do not possess acceptable physicochemical characteristics for passive permeability may utilize putative membrane transporters for CNS uptake. While both uptake and efflux transport mechanisms are expressed at the brain microvascular endothelium, uptake transporters can be targeted for optimization of brain drug delivery and improved treatment of neurological disease states. EXPERT OPINION Uptake transporters represent a unique opportunity to optimize brain drug delivery by leveraging the endogenous biology of the BBB. A rigorous understanding of these transporters is required to improve translation from the bench to clinical trials and stimulate the development of new treatment paradigms for neurological diseases.
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Affiliation(s)
| | - Thomas P. Davis
- Department of Pharmacology, University of Arizona College of Medicine
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Zhu JM, Chen C, Kong M, Zhu L, Li YL, Zhang JF, Yu ZP, Xu SS, Kong LY, Luo JG. Discovery and optimization of indirubin derivatives as novel ferroptosis inducers for the treatment of colon cancer. Eur J Med Chem 2023; 261:115829. [PMID: 37801824 DOI: 10.1016/j.ejmech.2023.115829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/16/2023] [Accepted: 09/21/2023] [Indexed: 10/08/2023]
Abstract
Glutathione peroxidase 4 (GPX4) is an essential antioxidant enzyme that negatively regulates ferroptosis. To exploit novel GPX4 inhibitors, we designed and synthesized 32 indirubin derivatives. Compound 31 exhibited the strongest antitumor activity against HCT-116 cells (IC50 = 0.49 ± 0.02 μM). Further studies suggested that 31 could induce ferroptosis in colon cancer cells and its cytotoxic activity could be reversed by ferroptosis inhibitors. Mechanism research showed that 31 promoted the degradation of GPX4, causing the accumulation of lipid ROS to induce ferroptosis. Animal experiments also proved that 31 could inhibit the growth of colon cancer cells in vivo and reduce the expression of GPX4 in tumor tissues. These results indicated that compound 31 had potential as a novel ferroptosis inducer agent for colon cancer.
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Affiliation(s)
- Jiang-Min Zhu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Chen Chen
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Min Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Ling Zhu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Ya-Lin Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Jian-Fei Zhang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Zhan-Peng Yu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Shi-Shu Xu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China
| | - Ling-Yi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China.
| | - Jian-Guang Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, People's Republic of China.
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Famuyiwa SO, Patil RB, Faloye KO, Awotuya IO, Gadhawe SP, Oladiran OJ, Bello OI. Sappanin-type homoisoflavonoids from Scilla nervosa inhibits acetylcholinesterase enzyme: a combined in silico and in vitro approach. J Biomol Struct Dyn 2023; 41:10957-10968. [PMID: 36940367 DOI: 10.1080/07391102.2023.2190825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/10/2022] [Indexed: 03/22/2023]
Abstract
Alzheimer's disease is among the major health challenges that currently attract the attention of health care givers and drug discovery and development experts worldwide. This study investigated the acetylcholinesterase inhibitory activity of sappanin-type homisoflavonoids isolated from the inter-bulb surface of Scilla nervosa. Molecular docking, molecular dynamics simulation, ADMET and in vitro studies were performed to identify the hit molecules, understand their binding mode and interaction, druggability and establish their inhibitory potentials against acetylcholinesterase enzyme. The hit compounds 5, 2, 1 and 4 were identified as the hit molecules through the molecular docking. The molecular dynamics simulation and MM-PBSA analysis showed the hit homoisoflavonoids established stability and good binding affinity against the acetylcholinesterase enzyme. Also, 5 elicited the best inhibitory activity followed by 2, 1 and 4 in the in vitro experiment. Furthermore, the selected homoisoflavonoids exhibit interesting drug likeness and pharmacokinetic properties as drug candidate. The results suggest further investigations towards the development of the phytochemicals as possible acetylcholinesterase inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Samson O Famuyiwa
- Department of Chemistry, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Rajesh B Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society's, Sinhgad College of Pharmacy, Pune, Maharashtra, India
| | - Kolade O Faloye
- Department of Chemistry, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Iyanu O Awotuya
- Department of Pharmaceutical Chemistry, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Sandeep P Gadhawe
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society's, Sinhgad College of Pharmacy, Pune, Maharashtra, India
| | - Oluyemi J Oladiran
- Department of Pharmacognosy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Oyenike I Bello
- Department of Pharmacognosy, Obafemi Awolowo University, Ile-Ife, Nigeria
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12
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Hossain MS, Roney M, Bin Mohd Yunus MY, Shariffuddin JH. Virtual screening, molecular docking, molecular dynamics, and MM-GBSA approaches identify prospective fructose-1,6-bisphosphatase inhibitors from pineapple for diabetes management. J Biomol Struct Dyn 2023:1-16. [PMID: 37916669 DOI: 10.1080/07391102.2023.2276889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
Abstract
Diabetes affects millions globally and poses treatment challenges. Targeting the enzyme fructose-1,6-bisphosphatase (FBPase) in gluconeogenesis and exploring plant-based therapies offer potential solutions for improving diabetes management while supporting sustainability and medicinal advancements. Utilizing pineapple (Ananas comosus L. Merr.) waste as a source of drug precursors could be valuable for health and environmental care due to its medicinal benefits and abundant yearly biomass production. Therefore, this study conducted a virtual screening to identify potential natural compounds from pineapple that could inhibit FBPase activity. A total of 112 compounds were screened for drug-likeness and ADMET properties, and molecular docking simulations were performed on 20 selected compounds using blind docking. The lead compound, butane-2,3-diyl diacetate, was subjected to 100 ns MD simulations, revealing a binding energy of -5.4 kcal/mol comparable to metformin (-5.6 kcal/mol). The MD simulation also confirmed stable complexes with crucial hydrogen bonds. Glu20, Ala24, Thr27, Gly28, Glu29, Leu30, Val160, Met177, Asp178, and Cys179 were identified as key amino acids that stabilized the human liver FBPase-butane-2,3-diyl diacetate complex, while Tyr215 and Asp218 played a crucial role in the human liver FBPase-Metformin complex. Our study indicates that the lead compound has high intestinal solubility. Therefore, it would show rapid bloodstream distribution and effective action on the target protein, making butane-2,3-diyl diacetate a potential antidiabetic drug candidate. However, further investigations in vitro, preclinical, and clinical trials are required to thoroughly assess its efficacy and safety.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Sanower Hossain
- Centre for Sustainability of Mineral and Resource Recovery Technology (Pusat SMaRRT), Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
| | - Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
| | - Mohd Yusri Bin Mohd Yunus
- Centre for Sustainability of Mineral and Resource Recovery Technology (Pusat SMaRRT), Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
| | - Jun Haslinda Shariffuddin
- Centre for Sustainability of Mineral and Resource Recovery Technology (Pusat SMaRRT), Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
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13
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Kus M, Ibragimow I, Piotrowska-Kempisty H. Caco-2 Cell Line Standardization with Pharmaceutical Requirements and In Vitro Model Suitability for Permeability Assays. Pharmaceutics 2023; 15:2523. [PMID: 38004503 PMCID: PMC10674574 DOI: 10.3390/pharmaceutics15112523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 11/26/2023] Open
Abstract
The Caco-2 cell line derived from human colon carcinoma is commonly used to assess the permeability of compounds in in vitro conditions. Due to the significant increase in permeability studies using the Caco-2 cell line in recent years, the need to standardize this biological model seems necessary. The pharmaceutical requirements define only the acceptance criteria for the validation of the Caco-2 cell line and do not specify the protocol for its implementation. Therefore, the aim of this study is to review the conditions for permeability studies across the Caco-2 monolayer reported in the available literature concerning validation guidelines. We summarized the main aspects affecting the validation process of the Caco-2 cell line, including the culture conditions, cytotoxicity, cell differentiation process, and monolayer transport conditions, and the main conclusions may be useful in developing individual methods for preparing the cell line for validation purposes and further permeability research.
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Affiliation(s)
- Marta Kus
- Department of Toxicology, Poznan University of Medical Sciences, 30 Dojazd St., 60-631 Poznan, Poland;
- Research and Development Department of Ethifarm, Ethifarm Manufacturing Plant, 9 Stefana Zeromskiego St., 60-544 Poznan, Poland;
| | - Izabela Ibragimow
- Research and Development Department of Ethifarm, Ethifarm Manufacturing Plant, 9 Stefana Zeromskiego St., 60-544 Poznan, Poland;
| | - Hanna Piotrowska-Kempisty
- Department of Toxicology, Poznan University of Medical Sciences, 30 Dojazd St., 60-631 Poznan, Poland;
- Department of Basic and Preclinical Science, Institute of Veterinary Medicine, Nicolaus Copernicus University in Toruń, 7 Gagarina St., 87-100 Torun, Poland
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14
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Ren R, Wang X, Leas DA, Scheurer C, Hoevel S, Cal M, Chen G, Zhong L, Katneni K, Pham T, Patil R, Sil D, Walters MJ, Schulze TT, Neville AJ, Dong Y, Wittlin S, Kaiser M, Davis PH, Charman SA, Vennerstrom JL. Antimalarial Dibenzannulated Medium-Ring Keto Lactams. ACS Infect Dis 2023; 9:1964-1980. [PMID: 37695781 PMCID: PMC10860121 DOI: 10.1021/acsinfecdis.3c00245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
We discovered dibenzannulated medium-ring keto lactams (11,12-dihydro-5H-dibenzo[b,g]azonine-6,13-diones) as a new antimalarial chemotype. Most of these had chromatographic LogD7.4 values ranging from <0 to 3 and good kinetic solubilities (12.5 to >100 μg/mL at pH 6.5). The more polar compounds in the series (LogD7.4 values of <2) had the best metabolic stability (CLint values of <50 μL/min/mg protein in human liver microsomes). Most of the compounds had relatively low cytotoxicity, with IC50 values >30 μM, and there was no correlation between antiplasmodial activity and cytotoxicity. The four most potent compounds had Plasmodium falciparum IC50 values of 4.2 to 9.4 nM and in vitro selectivity indices of 670 to >12,000. They were more than 4 orders-of-magnitude less potent against three other protozoal pathogens (Trypanosoma brucei rhodesiense, Trypanosoma cruzi, and Leishmania donovani) but did have relatively high potency against Toxoplasma gondii, with IC50 values ranging from 80 to 200 nM. These keto lactams are converted into their poorly soluble 4(1H)-quinolone transannular condensation products in vitro in culture medium and in vivo in mouse blood. The similar antiplasmodial potencies of three keto lactam-quinolone pairs suggest that the quinolones likely contribute to the antimalarial activity of the lactams.
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Affiliation(s)
- Rongguo Ren
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Xiaofang Wang
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Derek A Leas
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Christian Scheurer
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Sarah Hoevel
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Monica Cal
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Longjin Zhong
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Thao Pham
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Rahul Patil
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Diptesh Sil
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Matthias J Walters
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge St., Omaha, Nebraska 68182, United States
| | - Thomas T Schulze
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge St., Omaha, Nebraska 68182, United States
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, Nebraska 68198-5900, United States
| | - Andrew J Neville
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge St., Omaha, Nebraska 68182, United States
| | - Yuxiang Dong
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Sergio Wittlin
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Marcel Kaiser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Paul H Davis
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge St., Omaha, Nebraska 68182, United States
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Jonathan L Vennerstrom
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
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15
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Koziolek M, Augustijns P, Berger C, Cristofoletti R, Dahlgren D, Keemink J, Matsson P, McCartney F, Metzger M, Mezler M, Niessen J, Polli JE, Vertzoni M, Weitschies W, Dressman J. Challenges in Permeability Assessment for Oral Drug Product Development. Pharmaceutics 2023; 15:2397. [PMID: 37896157 PMCID: PMC10609725 DOI: 10.3390/pharmaceutics15102397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Drug permeation across the intestinal epithelium is a prerequisite for successful oral drug delivery. The increased interest in oral administration of peptides, as well as poorly soluble and poorly permeable compounds such as drugs for targeted protein degradation, have made permeability a key parameter in oral drug product development. This review describes the various in vitro, in silico and in vivo methodologies that are applied to determine drug permeability in the human gastrointestinal tract and identifies how they are applied in the different stages of drug development. The various methods used to predict, estimate or measure permeability values, ranging from in silico and in vitro methods all the way to studies in animals and humans, are discussed with regard to their advantages, limitations and applications. A special focus is put on novel techniques such as computational approaches, gut-on-chip models and human tissue-based models, where significant progress has been made in the last few years. In addition, the impact of permeability estimations on PK predictions in PBPK modeling, the degree to which excipients can affect drug permeability in clinical studies and the requirements for colonic drug absorption are addressed.
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Affiliation(s)
- Mirko Koziolek
- NCE Drug Product Development, Development Sciences, AbbVie Deutschland GmbH & Co. KG, 67061 Ludwigshafen, Germany
| | - Patrick Augustijns
- Drug Delivery and Disposition, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Constantin Berger
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, 97070 Würzburg, Germany;
| | - Rodrigo Cristofoletti
- Department of Pharmaceutics, University of Florida, 6550 Sanger Road, Orlando, FL 32827, USA
| | - David Dahlgren
- Department of Pharmaceutical Biosciences, Uppsala University, 75124 Uppsala, Sweden (J.N.)
| | - Janneke Keemink
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland;
| | - Pär Matsson
- Department of Pharmacology and SciLifeLab Gothenburg, University of Gothenburg, 40530 Gothenburg, Sweden;
| | - Fiona McCartney
- School of Veterinary Medicine, University College Dublin, D04 V1W8 Dublin, Ireland;
| | - Marco Metzger
- Translational Center for Regenerative Therapies (TLZ-RT) Würzburg, Branch of the Fraunhofer Institute for Silicate Research (ISC), 97082 Würzburg, Germany
| | - Mario Mezler
- Quantitative, Translational & ADME Sciences, AbbVie Deutschland GmbH & Co. KG, 67061 Ludwigshafen, Germany;
| | - Janis Niessen
- Department of Pharmaceutical Biosciences, Uppsala University, 75124 Uppsala, Sweden (J.N.)
| | - James E. Polli
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD 21021, USA;
| | - Maria Vertzoni
- Department of Pharmacy, National and Kapodistrian University of Athens, 157 84 Zografou, Greece;
| | - Werner Weitschies
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Jennifer Dressman
- Fraunhofer Institute of Translational Medicine and Pharmacology, 60596 Frankfurt, Germany
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16
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Murali M, Ahmed F, Gowtham HG, Aribisala JO, Abdulsalam RA, Shati AA, Alfaifi MY, Sayyed RZ, Sabiu S, Amruthesh KN. Exploration of CviR-mediated quorum sensing inhibitors from Cladosporium spp. against Chromobacterium violaceum through computational studies. Sci Rep 2023; 13:15505. [PMID: 37726386 PMCID: PMC10509224 DOI: 10.1038/s41598-023-42833-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/15/2023] [Indexed: 09/21/2023] Open
Abstract
An opportunistic human pathogenic bacterium, Chromobacterium violaceum resists the potency of most antibiotics by exploiting the quorum sensing system within their community to control virulence factor expression. Therefore, blocking the quorum sensing mechanism could help to treat several infectious caused by this organism. The quorum sensing receptor (CviR) of C. violaceum was used as a model target in the current investigation to identify potentially novel quorum sensing inhibitors from Cladosporium spp. through in silico computational approaches. The molecular docking results confirmed the anti-quorum sensing potential of bioactive compounds from Cladosporium spp. through binding to CviR with varying docking scores between - 5.2 and - 9.5 kcal/mol. Relative to the positive control [Azithromycin (- 7.4 kcal/mol)], the top six metabolites of Cladosporium spp. had higher docking scores and were generally greater than - 8.5 kcal/mol. The thermodynamic stability and binding affinity refinement of top-ranked CviR inhibitors were further studied through a 160 ns molecular dynamic (MD) simulation. The Post-MD simulation analysis confirmed the top-ranked compounds' affinity, stability, and biomolecular interactions with CviR at 50 ns, 100 ns, and 160 ns with Coniochaetone K of the Cladosporium spp. having the highest binding free energy (- 30.87 kcal/mol) and best interactions (two consistent hydrogen bond contact) following the 160 ns simulation. The predicted pharmacokinetics properties of top selected compounds point to their drug likeliness, potentiating their chance as a possible drug candidate. Overall, the top-ranked compounds from Cladosporium spp., especially Coniochaetone K, could be identified as potential C. violaceum CviR inhibitors. The development of these compounds as broad-spectrum antibacterial medicines is thus possible in the future following the completion of further preclinical and clinical research.
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Affiliation(s)
- Mahadevamurthy Murali
- Applied Plant Pathology Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysore, 570006, India
| | - Faiyaz Ahmed
- Department of Clinical Nutrition, College of Applied Health Sciences in Ar Rass, Qassim University, 51452, Buraydah, Saudi Arabia
| | | | - Jamiu Olaseni Aribisala
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Rukayat Abiola Abdulsalam
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Ali A Shati
- Faculty of Science, Biology Department, King Khalid University, 9004, Abha, Saudi Arabia
| | - Mohammad Y Alfaifi
- Faculty of Science, Biology Department, King Khalid University, 9004, Abha, Saudi Arabia
| | - R Z Sayyed
- Department of Microbiology, PSGVP Mandal's S I Patil Arts, G B Patel Science and STKV Sangh Commerce College, Shahada, 425409, India.
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa.
| | - Kestur Nagaraj Amruthesh
- Applied Plant Pathology Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysore, 570006, India.
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17
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Mizuno-Kaneko M, Hashimoto I, Miyahara K, Kochi M, Ohashi N, Tsumura K, Suzuki K, Tamura T. Molecular Design of Cyclic Peptides with Cell Membrane Permeability and Development of MDMX-p53 Inhibitor. ACS Med Chem Lett 2023; 14:1174-1178. [PMID: 37736191 PMCID: PMC10510666 DOI: 10.1021/acsmedchemlett.3c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 09/23/2023] Open
Abstract
Cyclic peptides have been expected to be one of the modalities of intracellular protein-protein interaction (PPI) inhibitors, but they are generally known to have low cell membrane permeability. In this study, we focused on the conformation of cyclic peptides in the cell membrane to determine the requirement for their cell membrane permeability through passive diffusion. Utilizing the requirement, we searched for structures with high affinity for MDMX via computational chemistry and acquired cyclic peptide 19 (Papp = 0.80 × 10-6 cm s-1, IC50 = 0.07 μM).
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Affiliation(s)
- Mai Mizuno-Kaneko
- Synthetic
Organic Chemistry Laboratories, FUJIFILM
Corporation, 577, Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa 258-8577, Japan
| | - Ichihiko Hashimoto
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Kenta Miyahara
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Masahiro Kochi
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Noriyuki Ohashi
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Kyosuke Tsumura
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Koo Suzuki
- Analysis
Technology Center, FUJIFILM Corporation, 210, Nakanuma, Minamiashigara-shi, Kanagawa 250-0193, Japan
| | - Takashi Tamura
- Synthetic
Organic Chemistry Laboratories, FUJIFILM
Corporation, 577, Ushijima, Kaisei-machi, Ashigarakami-gun, Kanagawa 258-8577, Japan
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18
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Diaz de Greñu B, Fernández-Aroca DM, Organero JA, Durá G, Jalón FA, Sánchez-Prieto R, Ruiz-Hidalgo MJ, Rodríguez AM, Santos L, Albasanz JL, Manzano BR. Ferrozoles: Ferrocenyl derivatives of letrozole with dual effects as potent aromatase inhibitors and cytostatic agents. J Biol Inorg Chem 2023; 28:531-547. [PMID: 37458856 DOI: 10.1007/s00775-023-02006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/07/2023] [Indexed: 08/11/2023]
Abstract
In the treatment of hormone-dependent cancers, aromatase inhibitors (AI) are receiving increased attention due to some undesirable effects such as the risk of endometrial cancer and thromboembolism of SERMs (selective estrogen receptor modulators). Letrozole is the most active AI with 99% aromatase inhibition. Unfortunately, this compound also exhibits some adverse effects such as hot flashes and fibromyalgias. Therefore, there is an urgent need to explore new types of AIs that retain the same-or even increased-antitumor ability. Inspired by the letrozole structure, a set of new derivatives has been synthesized that include a ferrocenyl moiety and different heterocycles. The derivative that contains a benzimidazole ring, namely compound 6, exhibits a higher aromatase inhibitory activity than letrozole and it also shows potent cytostatic behavior when compared to other well-established aromatase inhibitors, as demonstrated by dose-response, cell cycle, apoptosis and time course experiments. Furthermore, 6 promotes the inhibition of cell growth in both an aromatase-dependent and -independent fashion, as indicated by the study of A549 and MCF7 cell lines. Molecular docking and molecular dynamics calculations on the interaction of 6 or letrozole with the aromatase binding site revealed that the ferrocene moiety increases the van der Waals and hydrophobic interactions, thus resulting in an increase in binding affinity. Furthermore, the iron atom of the ferrocene fragment can form a metal-acceptor interaction with a propionate fragment, and this results in a stronger coupling with the heme group-a possibility that is consistent with the strong aromatase inhibition of 6.
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Affiliation(s)
- Borja Diaz de Greñu
- Departamento de Química Inorgánica, Orgánica y Bioquímica, Facultad de Ciencias y Tecnologías Químicas, IRICA, Universidad de Castilla-La Mancha, Avda. C. J Cela, 10, 13071, Ciudad Real, Spain
| | - Diego M Fernández-Aroca
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Albacete, Spain
| | - Juan A Organero
- Departamento de Química Física, Facultad de Ciencias Ambientales y Bioquímicas and INAMOL, Universidad de Castilla-La Mancha, 45071, Toledo, Spain
| | - Gema Durá
- Departamento de Química Inorgánica, Orgánica y Bioquímica, Facultad de Ciencias y Tecnologías Químicas, IRICA, Universidad de Castilla-La Mancha, Avda. C. J Cela, 10, 13071, Ciudad Real, Spain
| | - Felix Angel Jalón
- Departamento de Química Inorgánica, Orgánica y Bioquímica, Facultad de Ciencias y Tecnologías Químicas, IRICA, Universidad de Castilla-La Mancha, Avda. C. J Cela, 10, 13071, Ciudad Real, Spain
| | - Ricardo Sánchez-Prieto
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Albacete, Spain
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
- Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Albacete, Spain
| | - M José Ruiz-Hidalgo
- Laboratorio de Oncología Molecular, Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, Unidad Asociada de Biomedicina UCLM, Unidad Asociada al CSIC, Albacete, Spain
- Área de Bioquímica y Biología Molecular, Departamento de Química Inorgánica, Orgánica y Bioquímica, Facultad de Medicina, Universidad de Castilla-La Mancha, Albacete, Spain
| | - Ana María Rodríguez
- Departamento de Q. Inorgánica, Orgánica y Bioquímica, IRICA, Escuela Técnica Superior de Ingenieros Industriales, Universidad de Castilla-La Mancha, Avda. C. J. Cela, 3, 13071, Ciudad Real, Spain
| | - Lucia Santos
- Departamento de Q. Física, Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, Avda. C. J. Cela, S/N, 13071, Ciudad Real, Spain
| | - José L Albasanz
- Department of Inorganic and Organic Chemistry and Biochemistry, Faculty of Chemical and Technological Sciences, School of Medicine of Ciudad Real, Regional Center of Biomedical Research (CRIB), University of Castilla-La Mancha (UCLM), 13071, Ciudad Real, Spain
| | - Blanca R Manzano
- Departamento de Química Inorgánica, Orgánica y Bioquímica, Facultad de Ciencias y Tecnologías Químicas, IRICA, Universidad de Castilla-La Mancha, Avda. C. J Cela, 10, 13071, Ciudad Real, Spain.
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19
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Walker TWN, Schrodt F, Allard PM, Defossez E, Jassey VEJ, Schuman MC, Alexander JM, Baines O, Baldy V, Bardgett RD, Capdevila P, Coley PD, van Dam NM, David B, Descombes P, Endara MJ, Fernandez C, Forrister D, Gargallo-Garriga A, Glauser G, Marr S, Neumann S, Pellissier L, Peters K, Rasmann S, Roessner U, Salguero-Gómez R, Sardans J, Weckwerth W, Wolfender JL, Peñuelas J. Leaf metabolic traits reveal hidden dimensions of plant form and function. SCIENCE ADVANCES 2023; 9:eadi4029. [PMID: 37647404 PMCID: PMC10468135 DOI: 10.1126/sciadv.adi4029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
The metabolome is the biochemical basis of plant form and function, but we know little about its macroecological variation across the plant kingdom. Here, we used the plant functional trait concept to interpret leaf metabolome variation among 457 tropical and 339 temperate plant species. Distilling metabolite chemistry into five metabolic functional traits reveals that plants vary on two major axes of leaf metabolic specialization-a leaf chemical defense spectrum and an expression of leaf longevity. Axes are similar for tropical and temperate species, with many trait combinations being viable. However, metabolic traits vary orthogonally to life-history strategies described by widely used functional traits. The metabolome thus expands the functional trait concept by providing additional axes of metabolic specialization for examining plant form and function.
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Affiliation(s)
- Tom W. N. Walker
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Franziska Schrodt
- School of Geography, University of Nottingham, Nottingham NG7 2RD, UK
| | - Pierre-Marie Allard
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
| | - Emmanuel Defossez
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Vincent E. J. Jassey
- Laboratoire d’Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Meredith C. Schuman
- Departments of Geography and Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Jake M. Alexander
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Oliver Baines
- School of Geography, University of Nottingham, Nottingham NG7 2RD, UK
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | - Virginie Baldy
- Aix Marseille Université, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - Richard D. Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PT, UK
| | - Pol Capdevila
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona 08028, Spain
| | - Phyllis D. Coley
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Nicole M. van Dam
- Leibniz Institute of Vegetable and Ornamental crops (IGZ), 14979 Großbeeren, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Bruno David
- Green Mission Pierre Fabre, Institut de Recherche Pierre Fabre, 31562 Toulouse, France
| | - Patrice Descombes
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
- Ecosystems and Landscape Evolution, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), 8903 Birmensdorf, Switzerland
- Musée et Jardins botaniques cantonaux, 1007 Lausanne, Switzerland
| | - María-José Endara
- Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas, Universidad de Las Américas, 170124 Quito, Ecuador
| | - Catherine Fernandez
- Aix Marseille Université, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - Dale Forrister
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Albert Gargallo-Garriga
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08193 Bellaterra, Catalonia, Spain
- CREAF, 08193 Cerdanyola del Vallès, Catalonia, Spain
- Global Change Research Institute, Czech Academy of Sciences, 603 00 Brno, Czech Republic
| | - Gaëtan Glauser
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Sue Marr
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, 06120 Halle, Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle Wittenberg, 06108 Halle, Germany
| | - Steffen Neumann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, 06120 Halle, Germany
| | - Loïc Pellissier
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
- Ecosystems and Landscape Evolution, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), 8903 Birmensdorf, Switzerland
| | - Kristian Peters
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, 06120 Halle, Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle Wittenberg, 06108 Halle, Germany
| | - Sergio Rasmann
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Ute Roessner
- Research School of Biology, The Australian National University, 2601 Acton, Australia
| | | | - Jordi Sardans
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08193 Bellaterra, Catalonia, Spain
- CREAF, 08193 Cerdanyola del Vallès, Catalonia, Spain
| | - Wolfram Weckwerth
- Molecular Systems Biology, Department of Functional and Evolutionary Ecology, 1010 University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, 1010 University of Vienna, Vienna, Austria
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08193 Bellaterra, Catalonia, Spain
- CREAF, 08193 Cerdanyola del Vallès, Catalonia, Spain
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20
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Chen L, Fan Z, Chang J, Yang R, Hou H, Guo H, Zhang Y, Yang T, Zhou C, Sui Q, Chen Z, Zheng C, Hao X, Zhang K, Cui R, Zhang Z, Ma H, Ding Y, Zhang N, Lu X, Luo X, Jiang H, Zhang S, Zheng M. Sequence-based drug design as a concept in computational drug design. Nat Commun 2023; 14:4217. [PMID: 37452028 PMCID: PMC10349078 DOI: 10.1038/s41467-023-39856-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 06/27/2023] [Indexed: 07/18/2023] Open
Abstract
Drug development based on target proteins has been a successful approach in recent decades. However, the conventional structure-based drug design (SBDD) pipeline is a complex, human-engineered process with multiple independently optimized steps. Here, we propose a sequence-to-drug concept for computational drug design based on protein sequence information by end-to-end differentiable learning. We validate this concept in three stages. First, we design TransformerCPI2.0 as a core tool for the concept, which demonstrates generalization ability across proteins and compounds. Second, we interpret the binding knowledge that TransformerCPI2.0 learned. Finally, we use TransformerCPI2.0 to discover new hits for challenging drug targets, and identify new target for an existing drug based on an inverse application of the concept. Overall, this proof-of-concept study shows that the sequence-to-drug concept adds a perspective on drug design. It can serve as an alternative method to SBDD, particularly for proteins that do not yet have high-quality 3D structures available.
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Affiliation(s)
- Lifan Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Zisheng Fan
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Jiangsu, Nanjing, 210023, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, No. 393 Huaxia Middle Road, Shanghai, 200031, China
| | - Jie Chang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Jiangsu, Nanjing, 210023, China
| | - Ruirui Yang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, No. 393 Huaxia Middle Road, Shanghai, 200031, China
| | - Hui Hou
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Hao Guo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Yinghui Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Tianbiao Yang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Chenmao Zhou
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Jiangsu, Nanjing, 210023, China
| | - Qibang Sui
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Zhengyang Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Chen Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Xinyue Hao
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Jiangsu, Nanjing, 210023, China
| | - Keke Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Jiangsu, Nanjing, 210023, China
| | - Rongrong Cui
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Zehong Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Hudson Ma
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Yiluan Ding
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Naixia Zhang
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Xiaojie Lu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Xiaomin Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Jiangsu, Nanjing, 210023, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, No. 393 Huaxia Middle Road, Shanghai, 200031, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China
| | - Sulin Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Jiangsu, Nanjing, 210023, China.
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, No. 393 Huaxia Middle Road, Shanghai, 200031, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China.
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21
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Abdulredha FH, Mahdi MF, Khan AK. In silico evaluation of binding interaction and ADME study of new 1,3-diazetidin-2-one derivatives with high antiproliferative activity. J Adv Pharm Technol Res 2023; 14:176-184. [PMID: 37692021 PMCID: PMC10483897 DOI: 10.4103/japtr.japtr_116_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/01/2023] [Accepted: 06/07/2023] [Indexed: 09/12/2023] Open
Abstract
A series of eight novels' 1,3-diazetidin-2-ones have been proposed to assess their potential activities. They are intended to examine antiproliferative effects through inhibition of epidermal growth factor receptor (EGFR) expression. These eight compounds strongly interact with the EGFR protein, responsible for the activity. As part of a present study, these compounds were docked to the crystal structure of the EGFR (Protein Data Bank code: 1 M17) to determine their binding affinity at the active site. Based on computer predictions, two compounds were demonstrated high scores of 80.80 and 85.89. After analyzing ADME properties, these compounds were found to have significant potential for binding. Consequently, the abilities of gefitinib, erlotinib, imatinib, and sorafenib were selected for comparison as controls. Computational methods were performed to predict the critical disposition of eight novels' 1,3-diazetidin-2-one derivatives to the EGFR. Moreover, a docking technique employing the Genetic Optimization for Ligand Docking program was conducted. Compounds 2 and 7 demonstrate a high docking peace-wise scoring function (PLP) fitness of 85.89 and 80.80, respectively. They fulfilled the Lipinski's rule, topological descriptors, and fingerprints of drug-like molecular structure keys. These compounds can be used as lead compounds to develop novel antiproliferative agents. The outcome of applying this study is novel series of 1,3-diazetidin-2-one compounds as new analogs were designed and evaluated for their antiproliferative activity with a higher potency profile and binding affinity within the active sites of EGFR.
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Affiliation(s)
- Farah Haidar Abdulredha
- Department of Pharmaceutical Chemistry, College of Pharmacy, Al-Mustansiriyah University, Baghdad, Iraq
| | - Monther Faisal Mahdi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Al-Mustansiriyah University, Baghdad, Iraq
| | - Ayad Kareem Khan
- Department of Pharmaceutical Chemistry, College of Pharmacy, Al-Mustansiriyah University, Baghdad, Iraq
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22
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Wermelinger GF, Rubini L, da Fonseca ACC, Ouverney G, de Oliveira RPRF, de Souza AS, Forezi LSM, Limaverde-Sousa G, Pinheiro S, Robbs BK. A Novel MDM2-Binding Chalcone Induces Apoptosis of Oral Squamous Cell Carcinoma. Biomedicines 2023; 11:1711. [PMID: 37371806 DOI: 10.3390/biomedicines11061711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) represents ~90% of all oral cancers, being the eighth most common cancer in men. The overall 5-year survival rate is only 39% for metastatic cancers, and currently used chemotherapeutics can cause important side effects. Thus, there is an urgency in developing new and effective anti-cancer agents. As both chalcones and 1,2,3-triazoles are valuable pharmacophores/privileged structures in the search for anticancer compounds, in this work, new 1,2,3-triazole-chalcone hybrids were synthesized and evaluated against oral squamous cell carcinoma. By using different in silico, in vitro, and in vivo approaches, we demonstrated that compound 1f has great cytotoxicity and selectivity against OSCC (higher than carboplatin and doxorubicin) and other cancer cells in addition to showing minimal toxicity in mice. Furthermore, we demonstrate that induced cell death occurs by apoptosis and cell cycle arrest at the G2/M phase. Moreover, we found that 1f has a potential affinity for MDM2 protein, similar to the known ligand nutlin-3, and presents a better selectivity, pharmacological profile, and potential to be orally absorbed and is not a substrate of Pg-P when compared to nutlin-3. Therefore, we conclude that 1f is a good lead for a new chemotherapeutic drug against OSCC and possibly other types of cancers.
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Affiliation(s)
- Guilherme Freimann Wermelinger
- Basic Science Department, Health Institute of Nova Friburgo, Fluminense Federal University, Nova Friburgo 28625-650, RJ, Brazil
| | - Lucas Rubini
- Basic Science Department, Health Institute of Nova Friburgo, Fluminense Federal University, Nova Friburgo 28625-650, RJ, Brazil
| | - Anna Carolina Carvalho da Fonseca
- Postgraduate Program in Dentistry, Health Institute of Nova Friburgo, Fluminense Federal University, Nova Friburgo 28625-650, RJ, Brazil
| | - Gabriel Ouverney
- Postgraduate Program in Applied Science for Health Products, Faculty of Pharmacy, Fluminense Federal University, Niteroi 24020-141, RJ, Brazil
| | - Rafael P R F de Oliveira
- Department of Organic Chemistry, Chemistry Institute, Fluminense Federal University, Niteroi 24020-141, RJ, Brazil
| | - Acácio S de Souza
- Department of Organic Chemistry, Chemistry Institute, Fluminense Federal University, Niteroi 24020-141, RJ, Brazil
| | - Luana S M Forezi
- Department of Organic Chemistry, Chemistry Institute, Fluminense Federal University, Niteroi 24020-141, RJ, Brazil
| | - Gabriel Limaverde-Sousa
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21040-900, RJ, Brazil
| | - Sergio Pinheiro
- Department of Organic Chemistry, Chemistry Institute, Fluminense Federal University, Niteroi 24020-141, RJ, Brazil
| | - Bruno Kaufmann Robbs
- Basic Science Department, Health Institute of Nova Friburgo, Fluminense Federal University, Nova Friburgo 28625-650, RJ, Brazil
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23
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Malik MS, Faazil S, Alsharif MA, Sajid Jamal QM, Al-Fahemi JH, Banerjee A, Chattopadhyay A, Pal SK, Kamal A, Ahmed SA. Antibacterial Properties and Computational Insights of Potent Novel Linezolid-Based Oxazolidinones. Pharmaceuticals (Basel) 2023; 16:ph16040516. [PMID: 37111273 PMCID: PMC10143092 DOI: 10.3390/ph16040516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The mounting evidence of bacterial resistance against commonly prescribed antibiotics warrants the development of new antibacterial drugs on an urgent basis. Linezolid, an oxazolidinone antibiotic, is a lead molecule in designing new oxazolidinones as antibacterial agents. In this study, we report the antibacterial potential of the novel oxazolidinone-sulphonamide/amide conjugates that were recently reported by our research group. The antibacterial assays showed that, from the series, oxazolidinones 2 and 3a exhibited excellent potency (MIC of 1.17 μg/mL) against B. subtilis and P. aeruginosa strains, along with good antibiofilm activity. Docking studies revealed higher binding affinities of oxazolidinones 2 and 3a compared to linezolid, which were further validated by molecular dynamics simulations. In addition to this, other computational studies, one-descriptor (log P) analysis, ADME-T and drug likeness studies demonstrated the potential of these novel linezolid-based oxazolidinones to be taken forward for further studies.
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24
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Design, Synthesis, In Silico and POM Studies for the Identification of the Pharmacophore Sites of Benzylidene Derivatives. Molecules 2023; 28:molecules28062613. [PMID: 36985587 PMCID: PMC10053039 DOI: 10.3390/molecules28062613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
Due to the uneven distribution of glycosidase enzyme expression across bacteria and fungi, glycoside derivatives of antimicrobial compounds provide prospective and promising antimicrobial materials. Therefore, herein, we report the synthesis and characterization of six novel methyl 4,6-O-benzylidene-α-d-glucopyranoside (MBG) derivatives (2–7). The structures were ascertained using spectroscopic techniques and elemental analyses. Antimicrobial tests (zone of inhibition, MIC and MBC) were carried out to determine their ability to inhibit the growth of different Gram-positive, Gram-negative bacteria and fungi. The highest antibacterial activity was recorded with compounds 4, 5, 6 and 7. The compounds with the most significant antifungal efficacy were 4, 5, 6 and 7. Based on the prediction of activity spectra for substances (PASS), compounds 4 and 7 have promising antimicrobial capacity. Molecular docking studies focused on fungal and bacterial proteins where derivatives 3 and 6 exhibited strong binding affinities. The molecular dynamics study revealed that the complexes formed by these derivatives with the proteins L,D-transpeptidase Ykud and endoglucanase from Aspergillus niger remained stable, both over time and in physiological conditions. Structure–activity relationships, including in vitro and in silico results, revealed that the acyl chains [lauroyl-(CH3(CH2)10CO-), cinnamoyl-(C6H5CH=CHCO-)], in combination with sugar, were found to have the most potential against human and fungal pathogens. Synthetic, antimicrobial and pharmacokinetic studies revealed that MBG derivatives have good potential for antimicrobial activity, developing a therapeutic target for bacteria and fungi. Furthermore, the Petra/Osiris/Molinspiration (POM) study clearly indicated the presence of an important (O1δ−----O2δ−) antifungal pharmacophore site. This site can also be explored as a potential antiviral moiety.
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25
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Dorel R, Wong AR, Crawford JJ. Trust Your Gut: Strategies and Tactics for Intestinally Restricted Drugs. ACS Med Chem Lett 2023; 14:233-243. [PMID: 36923921 PMCID: PMC10009798 DOI: 10.1021/acsmedchemlett.3c00001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/02/2023] [Indexed: 02/24/2023] Open
Abstract
Non-absorbable small-molecule drugs targeted to the gut represent an alternative approach to safe, non-systemic therapeutics. Such drugs remain confined to the gastrointestinal tract upon oral dosing by virtue of their limited passive permeability, increasing the local concentration at the site of action while minimizing exposure elsewhere in the body. Herein we review the latest advances in the field of gut-restricted therapeutics, highlighting the different strategies and tactics that medicinal chemists have employed in pursuit of drugs with minimal intestinal absorption.
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Affiliation(s)
- Ruth Dorel
- Genentech, Inc., South San Francisco, California 94080, United States
| | - Alice R. Wong
- Genentech, Inc., South San Francisco, California 94080, United States
| | - James J. Crawford
- Genentech, Inc., South San Francisco, California 94080, United States
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26
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Wieske LHE, Atilaw Y, Poongavanam V, Erdélyi M, Kihlberg J. Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds. Chemistry 2023; 29:e202202798. [PMID: 36286339 PMCID: PMC10107787 DOI: 10.1002/chem.202202798] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to adjust conformations in response to the polarity of the environment, i.e. molecular chameleonicity, is considered to be important for conferring both high aqueous solubility and high cell permeability to drugs in chemical space beyond Lipinski's rule of 5. We determined the conformational ensembles populated by the antiviral drugs asunaprevir, simeprevir, atazanavir and daclatasvir in polar (DMSO-d6 ) and non-polar (chloroform) environments with NMR spectroscopy. Daclatasvir was fairly rigid, whereas the first three showed large flexibility in both environments, that translated into major differences in solvent accessible 3D polar surface area within each conformational ensemble. No significant differences in size and polar surface area were observed between the DMSO-d6 and chloroform ensembles of these three drugs. We propose that such flexible compounds are characterized as "partial molecular chameleons" and hypothesize that their ability to adopt conformations with low polar surface area contributes to their membrane permeability and oral absorption.
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Affiliation(s)
- Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | | | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
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Ilhan S, Atmaca H, Yilmaz ES, Korkmaz E, Zora M. N-Propargylic β-enaminones in breast cancer cells: Cytotoxicity, apoptosis, and cell cycle analyses. J Biochem Mol Toxicol 2023; 37:e23299. [PMID: 36647602 DOI: 10.1002/jbt.23299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/30/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023]
Abstract
Breast cancer is one of the most common cancers worldwide and the discovery of new cytotoxic agents is needed. Enaminones are regarded to be a significant structural motif that is found in a variety of pharmacologically active compounds however the number of studies investigating the anticancer activities of N-propargylic β-enaminones (NPEs) is limited. Herein we investigated the potential cytotoxic and apoptotic effects of 23 different NPEs (1-23) on human breast cancer cells. Cytotoxicity was evaluated via MTT assay. Apoptotic cell death and cell cycle distributions were investigated by flow cytometry. CM-H2DCFDA dye was used to evaluate cellular ROS levels. Expression levels of Bcl-2, Bax, p21, and Cyclin D1 were measured by quantitative real-time PCR. ADME properties were calculated using the ADMET 2.0 tool. NPEs 4, 9, 16, and 21 showed selective cytotoxic activity against breast cancer cells with SI values >2. NPEs induced apoptosis and caused significant changes in Bcl-2 and Bax mRNA levels. The cell cycle was arrested at the G0/G1 phase and levels of p21 and Cyclin D1 were upregulated in both breast cancer cells. ROS levels were significantly increased by NPEs, suggesting that the cytotoxic and apoptotic effects of NPEs were mediated by ROS. ADME analysis revealed that NPEs showed favorable distributions in both breast cancer cell lines, meaning good lipophilicity values, low unfractionated values, and high bioavailability. Therefore, these potential anticancer compounds should be further validated by in vivo studies for their appropriate function in human health with a safety profile, and a comprehensive drug interaction study should be performed.
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Affiliation(s)
- Suleyman Ilhan
- Department of Biology, Faculty of Science and Letters, Celal Bayar University, Manisa, Turkey
| | - Harika Atmaca
- Department of Biology, Faculty of Science and Letters, Celal Bayar University, Manisa, Turkey
| | - Elif Serel Yilmaz
- Department of Chemistry, Middle East Technical University, Ankara, Turkey
| | - Esra Korkmaz
- Department of Chemistry, Middle East Technical University, Ankara, Turkey
| | - Metin Zora
- Department of Chemistry, Middle East Technical University, Ankara, Turkey
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Effect of the Addition of the Fifth Amino Acid to [GADV]-Protein on the Three-Dimensional Structure. LIFE (BASEL, SWITZERLAND) 2023; 13:life13010246. [PMID: 36676195 PMCID: PMC9863117 DOI: 10.3390/life13010246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023]
Abstract
The [GADV]-protein, consisting only of glycine (G), alanine (A), aspartic acid (D), and valine (V), is frequently studied as a candidate for a primitive protein that existed at the beginning of life on Earth. The number of proteogenic amino acids increased during evolution, and glutamic acid may have been added as the fifth amino acid. In this study, we used molecular dynamics simulations to estimate the conformation of random peptides when glutamate is added to G, A, D, and V ([GADVE]), when leucine is added ([GADVL]), and when the frequency of alanine is doubled ([GADVA]). The results showed that the secondary structure contents of the [GADVE]-peptide and [GADVL]-peptide were higher than that of the [GADVA]-peptide. Although the [GADVL]-peptide had a higher secondary structure formation ability than the [GADVE]-peptide, it was less water soluble, suggesting that it may not be a primitive protein. The [GA(D/E)V]-peptide with G:A:D:V:E = 2:2:1:2:1 according to the occurrence ratio in the codon table also increased the secondary structure contents compared to the [GADV]-peptide, indicating that the addition of glutamic acid increased the structure formation ability of the primitive protein candidates.
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Roney M, Huq AKMM, Issahaku AR, Soliman MES, Hossain MS, Mustafa AH, Islam MA, Dubey A, Tufail A, Mohd Aluwi MFF, Tajuddin SN. Pharmacophore-based virtual screening and in-silico study of natural products as potential DENV-2 RdRp inhibitors. J Biomol Struct Dyn 2023; 41:12186-12203. [PMID: 36645141 DOI: 10.1080/07391102.2023.2166123] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/01/2023] [Indexed: 01/17/2023]
Abstract
Dengue fever is a significant public health concern throughout the world, causing an estimated 500,000 hospitalizations and 20,000 deaths each year, despite the lack of effective therapies. The DENV-2 RdRp has been identified as a potential target for the development of new and effective dengue therapies. This research's primary objective was to discover an anti-DENV inhibitor using in silico ligand- and structure-based approaches. To begin, a ligand-based pharmacophore model was developed, and 130 distinct natural products (NPs) were screened. Docking of the pharmacophore-matched compounds were performed to the active site of DENV-2 RdRp protease . Eleven compounds were identified as potential DENV-2 RdRp inhibitors based on docking energy and binding interactions. ADMET and drug-likeness were done to predict their pharmacologic, pharmacokinetic, and drug-likeproperties . Compounds ranked highest in terms of pharmacokinetics and drug-like appearances were then subjected to additional toxicity testing to determine the leading compound. Additionally, MD simulation of the lead compound was performed to confirm the docked complex's stability and the binding site determined by docking. As a result, the lead compound (compound-108) demonstrated an excellent match to the pharmacophore, a strong binding contact and affinity for the RdRp enzyme, favourable pharmacokinetics, and drug-like characteristics. In summary, the lead compound identified in this study could be a possible DENV-2 RdRp inhibitor that may be further studied on in vitro and in vivo models to develop as a drug candidate.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Kuantan, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Kuantan, Malaysia
| | - A K M Moyeenul Huq
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Kuantan, Malaysia
- School of Medicine, Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Abdul Rashid Issahaku
- West African Centre for Computational Analysis, Ghana
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Md Sanower Hossain
- Centre for Sustainability of Ecosystem and Earth Resources (Pusat ALAM), Universiti Malaysia Pahang, Kuantan, Malaysia
- Faculty of Science, Sristy College of Tangail, Tangail, Bangladesh
| | - Abu Hasnat Mustafa
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Kuantan, Malaysia
| | - Md Alimul Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Amit Dubey
- Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, India
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Aisha Tufail
- Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, India
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Kuantan, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Kuantan, Malaysia
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Luo J, Wen W, Chen J, Zeng X, Wang P, Xu S. Differences in tissue distribution ability of evodiamine and dehydroevodiamine are due to the dihedral angle of the molecule stereo-structure. Front Pharmacol 2023; 14:1109279. [PMID: 37089948 PMCID: PMC10117637 DOI: 10.3389/fphar.2023.1109279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
Introduction: This researcher focused at the evodiamine and dehydroevodiamine tissue distribution and structure-pharmacokinetics (PK) relationship after intravenous injection in mice. Methods: Using a transmembrane transport experiment, the permeability of evodiamine and dehydroevodiamine on Caco-2 cells was evaluated. The tissue distribution and pharmacokinetics (PK) of evodiamine and dehydroevodiamine in mice were studied. To comprehend the connection between structure and tissue distribution, physicochemical property evaluations and molecular electrostatic potential (MEP) calculations were performed. Results: Dehydroevodiamine's Papp values in vitro were 10-5 cm/s, whereas evodiamine's were 10-6 cm/s. At a dose of 5 mg/kg, the brain concentration of dehydroevodiamine was 6.44 times more than that of evodiamine. By MEP or physicochemical measures, the permeability difference between evodiamine and dehydroevodiamine is unaffected. The dihedral angle of the stereo-structure appears to be the main cause of the difference in tissue distribution ability between evodiamine and dehydroevodiamine. Discussion: Dehydroevodiamine has a dihedral angle of 3.71° compared to 82.34° for evodiamine. Dehydroevodiamine can more easily pass through the phospholipid bilayer than evodiamine because it has a more planar stereo-structure. Dehydroevodiamine is therefore more likely to pass cross the blood-brain barrier and enter the brain in a tissue-specific manner.
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Affiliation(s)
- Jie Luo
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Wen Wen
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jie Chen
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xiaobo Zeng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Ping Wang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- *Correspondence: Ping Wang, ; Shijun Xu,
| | - Shijun Xu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- *Correspondence: Ping Wang, ; Shijun Xu,
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Borges AA, de Souza MP, da Fonseca ACC, Wermelinger GF, Ribeiro RCB, Amaral AAP, de Carvalho CJC, Abreu LS, de Queiroz LN, de Almeida ECP, Rabelo VW, Abreu PA, Pontes B, Ferreira VF, da Silva FDC, Forezi LDSM, Robbs BK. Chemoselective Synthesis of Mannich Adducts from 1,4-Naphthoquinones and Profile as Autophagic Inducers in Oral Squamous Cell Carcinoma. Molecules 2022; 28:molecules28010309. [PMID: 36615502 PMCID: PMC9822194 DOI: 10.3390/molecules28010309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 01/03/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a worldwide public health problem, accounting for approximately 90% of all oral cancers, and is the eighth most common cancer in men. Cisplatin and carboplatin are the main chemotherapy drugs used in the clinic. However, in addition to their serious side effects, such as damage to the nervous system and kidneys, there is also drug resistance. Thus, the development of new drugs becomes of great importance. Naphthoquinones have been described with antitumor activity. Some of them are found in nature, but semi synthesis has been used as strategy to find new chemical entities for the treatment of cancer. In the present study, we promote a multiple component reaction (MCR) among lawsone, arylaldehydes, and benzylamine to produce sixteen chemoselectively derivated Mannich adducts of 1,4-naphthoquinones in good yield (up to 97%). The antitumor activities and molecular mechanisms of action of these compounds were investigated in OSCC models and the compound 6a induced cytotoxicity in three different tumor cell lines (OSCC4, OSCC9, and OSCC25) and was more selective (IS > 2) for tumor cells than the chemotropic drug carboplatin and the controls lapachol and shikonin, which are chemically similar compounds with cytotoxic effects. The 6a selectively and significantly reduced the amount of cell colony growth, was not hemolytic, and tolerable in mice with no serious side effects at a concentration of 100 mg/kg with a LD50 of 150 mg/kg. The new compound is biologically stable with a profile similar to carboplatin. Morphologically, 6a does not induce cell retraction or membrane blebs, but it does induce intense vesicle formation and late emergence of membrane bubbles. Exploring the mechanism of cell death induction, compound 6a does not induce ROS formation, and cell viability was not affected by inhibitors of apoptosis (ZVAD) and necroptosis (necrostatin 1). Autophagy followed by a late apoptosis process appears to be the death-inducing pathway of 6a, as observed by increased viability by the autophagy inhibitor (3-MA) and by the appearance of autophagosomes, later triggering a process of late apoptosis with the presence of caspase 3/7 and DNA fragmentation. Molecular modeling suggests the ability of the compound to bind to topoisomerase I and II and with greater affinity to hPKM2 enzyme than controls, which could explain the mechanism of cell death by autophagy. Finally, the in-silico prediction of drug-relevant properties showed that compound 6a has a good pharmacokinetic profile when compared to carboplatin and doxorubicin. Among the sixteen naphthoquinones tested, compound 6a was the most effective and is highly selective and well tolerated in animals. The induction of cell death in OSCC through autophagy followed by late apoptosis possibly via inhibition of the PKM2 enzyme points to a promising potential of 6a as a new preclinical anticancer candidate.
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Affiliation(s)
- Amanda A. Borges
- Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, Universidade Federal Fluminense, Niterói CEP 24020-150, Brazil
| | - Michele P. de Souza
- Programa de Pós-Graduação em Ciências Aplicadas a Produtos para Saúde, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói CEP 24241-000, Brazil
| | - Anna Carolina C. da Fonseca
- Programa de Pós-Graduação em Odontologia, Instituto de Saúde de Nova Friburgo, Universidade Federal Fluminense, Nova Friburgo CEP 28625-650, Brazil
| | - Guilherme F. Wermelinger
- Departamento de Ciência Básica, Campus Universitário de Nova Friburgo, Universidade Federal Fluminense, Nova Friburgo CEP 28625-650, Brazil
| | - Ruan C. B. Ribeiro
- Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, Universidade Federal Fluminense, Niterói CEP 24020-150, Brazil
| | - Adriane A. P. Amaral
- Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, Universidade Federal Fluminense, Niterói CEP 24020-150, Brazil
| | - Cláudio José C. de Carvalho
- Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, Universidade Federal Fluminense, Niterói CEP 24020-150, Brazil
| | - Lucas S. Abreu
- Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, Universidade Federal Fluminense, Niterói CEP 24020-150, Brazil
| | - Lucas Nicolau de Queiroz
- Programa de Pós-Graduação em Ciências Aplicadas a Produtos para Saúde, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói CEP 24241-000, Brazil
| | - Elan C. P. de Almeida
- Departamento de Ciência Básica, Campus Universitário de Nova Friburgo, Universidade Federal Fluminense, Nova Friburgo CEP 28625-650, Brazil
| | - Vitor W. Rabelo
- Instituto de Biodiversidade e Sustentabilidade, Campus Macaé, Universidade Federal do Rio de Janeiro, Macaé CEP 27965-045, Brazil
| | - Paula A. Abreu
- Instituto de Biodiversidade e Sustentabilidade, Campus Macaé, Universidade Federal do Rio de Janeiro, Macaé CEP 27965-045, Brazil
| | - Bruno Pontes
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro CEP 21941-902, Brazil
| | - Vitor F. Ferreira
- Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói CEP 24241-000, Brazil
| | - Fernando de C. da Silva
- Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, Universidade Federal Fluminense, Niterói CEP 24020-150, Brazil
| | - Luana da S. M. Forezi
- Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, Universidade Federal Fluminense, Niterói CEP 24020-150, Brazil
- Correspondence: (L.d.S.M.F.); (B.K.R.)
| | - Bruno K. Robbs
- Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, Universidade Federal Fluminense, Niterói CEP 24020-150, Brazil
- Correspondence: (L.d.S.M.F.); (B.K.R.)
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32
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Bultum LE, Tolossa GB, Kim G, Kwon O, Lee D. In silico activity and ADMET profiling of phytochemicals from Ethiopian indigenous aloes using pharmacophore models. Sci Rep 2022; 12:22221. [PMID: 36564437 PMCID: PMC9789083 DOI: 10.1038/s41598-022-26446-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
In silico profiling is used in identification of active compounds and guide rational use of traditional medicines. Previous studies on Ethiopian indigenous aloes focused on documentation of phytochemical compositions and traditional uses. In this study, ADMET and drug-likeness properties of phytochemicals from Ethiopian indigenous aloes were evaluated, and pharmacophore-based profiling was done using Discovery Studio to predict therapeutic targets. The targets were examined using KEGG pathway, gene ontology and network analysis. Using random-walk with restart algorithm, network propagation was performed in CODA network to find diseases associated with the targets. As a result, 82 human targets were predicted and found to be involved in several molecular functions and biological processes. The targets also were linked to various cancers and diseases of immune system, metabolism, neurological system, musculoskeletal system, digestive system, hematologic, infectious, mouth and dental, and congenital disorder of metabolism. 207 KEGG pathways were enriched with the targets, and the main pathways were metabolism of steroid hormone biosynthesis, lipid and atherosclerosis, chemical carcinogenesis, and pathways in cancer. In conclusion, in silico target fishing and network analysis revealed therapeutic activities of the phytochemicals, demonstrating that Ethiopian indigenous aloes exhibit polypharmacology effects on numerous genes and signaling pathways linked to many diseases.
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Affiliation(s)
- Lemessa Etana Bultum
- grid.37172.300000 0001 2292 0500Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291Daehak-Ro, Daejeon, 34141 South Korea ,Bio-Synergy Research Center, 291Daehak-Ro, Daejeon, 34141 South Korea ,grid.255166.30000 0001 2218 7142Department of Applied Bioscience, Dong-A Universtiy, Busan 49315, South Korea
| | - Gemechu Bekele Tolossa
- Bio-Synergy Research Center, 291Daehak-Ro, Daejeon, 34141 South Korea ,grid.4367.60000 0001 2355 7002Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Gwangmin Kim
- grid.37172.300000 0001 2292 0500Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291Daehak-Ro, Daejeon, 34141 South Korea ,Bio-Synergy Research Center, 291Daehak-Ro, Daejeon, 34141 South Korea
| | - Ohhyeon Kwon
- grid.37172.300000 0001 2292 0500Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291Daehak-Ro, Daejeon, 34141 South Korea ,Bio-Synergy Research Center, 291Daehak-Ro, Daejeon, 34141 South Korea
| | - Doheon Lee
- grid.37172.300000 0001 2292 0500Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291Daehak-Ro, Daejeon, 34141 South Korea ,Bio-Synergy Research Center, 291Daehak-Ro, Daejeon, 34141 South Korea
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Calabretta LO, Yang J, Raines RT. N α -Methylation of arginine: Implications for cell-penetrating peptides. J Pept Sci 2022; 29:e3468. [PMID: 36494904 PMCID: PMC10073267 DOI: 10.1002/psc.3468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
The field of cell-penetrating peptides is dominated by the use of oligomers of arginine residues. Octanol-water partitioning in the presence of an anionic lipid is a validated proxy for cell-penetrative efficacy. Here, we add one, two, or three N-methyl groups to Ac-Arg-NH2 and examine the effects on octanol-water partitioning. In the absence of an anionic lipid, none of these arginine derivatives can be detected in the octanol layer. In the presence of sodium dodecanoate, however, increasing N-methylation correlates with increasing partitioning into octanol, which is predictive of higher cell-penetrative ability. We then evaluated fully Nα -methylated oligoarginine peptides and observed an increase in their cellular penetration compared with canonical oligoarginine peptides in some contexts. These findings indicate that a simple modification, Nα -methylation, can enhance the performance of cell-penetrating peptides.
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Affiliation(s)
- Lindsey O Calabretta
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jinyi Yang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Li N, Yang J, Wang C, Wu L, Liu Y. Screening bifunctional flavonoids of anti-cholinesterase and anti-glucosidase by in vitro and in silico studies: Quercetin, kaempferol and myricetin. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Kawamura M, Kobashi Y, Tanaka H, Bohno-Mikami A, Hamada M, Ito Y, Hirata T, Ohara H, Kojima N, Koretsune H, Gunji E, Fukunaga T, Inatani S, Hasegawa Y, Suzuki A, Takahashi T, Kakinuma H. Discovery of Novel Pyrazolylpyridine Derivatives for 20-Hydroxyeicosatetraenoic Acid Synthase Inhibitors with Selective CYP4A11/4F2 Inhibition. J Med Chem 2022; 65:14599-14613. [DOI: 10.1021/acs.jmedchem.2c01089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Madoka Kawamura
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Yohei Kobashi
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Hiroaki Tanaka
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Ayako Bohno-Mikami
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Makoto Hamada
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Yuji Ito
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Takashi Hirata
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Hiroki Ohara
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Naoki Kojima
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Hiroko Koretsune
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Emi Gunji
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Takuya Fukunaga
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Shoko Inatani
- Drug Safety and Pharmacokinetics Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Yoshitaka Hasegawa
- Drug Safety and Pharmacokinetics Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Akinori Suzuki
- Pharmaceutical Sciences Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Teisuke Takahashi
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Hiroyuki Kakinuma
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
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36
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Duarte DJ, Oldenkamp R, Ragas AMJ. Human health risk assessment of pharmaceuticals in the European Vecht River. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2022; 18:1639-1654. [PMID: 35112470 PMCID: PMC9790459 DOI: 10.1002/ieam.4588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/17/2022] [Accepted: 01/26/2022] [Indexed: 05/23/2023]
Abstract
Active pharmaceutical ingredients (APIs) can reach surface waters used for drinking water extraction and recreational activities, such as swimming and fishing. The aim of the present study was to systematically assess the lifetime human health risks posed by 15 individual APIs and their mixtures occurring in the German-Dutch transboundary Vecht River. An exposure model was developed and used to assess the combined risks of oral and dermal exposure under a variety of exposure conditions. A total of 4500 API uptake values and 165 lifetime risk values were estimated for 15 and 11 APIs, respectively. Overall, the lifetime human health risks posed by the APIs and their mixtures based on modeling results were deemed acceptable under typical exposure conditions. Under very extreme environmental conditions and human behavior, API mixture risks were of potential concern while the risks of individual APIs were negligible, with a few exceptions. The antibiotic doxycycline and analgesic phenazone showed the highest and lowest risks, respectively. The study did not evaluate the potential risks caused by metabolite compounds. Recommendations for water managers are provided to help improve the accuracy and utility of human health risk assessments of pharmaceuticals. Integr Environ Assess Manag 2022;18:1639-1654. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).
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Affiliation(s)
- Daniel J. Duarte
- Department of Environmental Science, Institute for Water & Wetland ResearchRadboud University NijmegenNijmegenThe Netherlands
| | - Rik Oldenkamp
- Department of Global Health‐Amsterdam, Institute for Global Health and Development, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Ad M. J. Ragas
- Department of Environmental Science, Institute for Water & Wetland ResearchRadboud University NijmegenNijmegenThe Netherlands
- Department of Environmental Sciences, Faculty of ScienceOpen UniversityHeerlenThe Netherlands
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37
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Alimardan Z, Abbasi M, Khodarahmi G, Kashfi K, Hasanzadeh F, Mahmud A. Identification of new small molecules as dual FoxM1 and Hsp70 inhibitors using computational methods. Res Pharm Sci 2022; 17:635-656. [PMID: 36704430 PMCID: PMC9872178 DOI: 10.4103/1735-5362.359431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/15/2022] [Accepted: 08/31/2022] [Indexed: 11/05/2022] Open
Abstract
Background and purpose FoxM1 and Hsp70 proteins are highly expressed in many cancers. Thus, their inhibition serves as Bonafede targets in cancer treatment. Experimental approach FDI-6, an inhibitor of FoxM1, was selected as a template, and based on its structure, a new library from the ZINC database was obtained. Virtual screening was then performed using the created pharmacophore model. The second virtual screening phase was conducted with molecular docking to get the best inhibitor for both FoxM1 and Hsp70 active sites. In silico, ADMET properties were also calculated. Finally, molecular dynamics simulation was performed on the best ligand, ZINC1152745, for both Hsp70 and FoxM1 proteins during 100 ns. Findings / Results The results of this study indicated that ZINC1152745 was stable in the active site of both proteins, Hsp70 and FoxM1. The final scaffold identified by the presented computational approach could offer a hit compound for designing promising anticancer agents targeting both FoxM1 and Hsp70. Conclusion and implications Molecular dynamics simulations were performed on ZINC1152745 targeting FoxM1 and Hsp70 active sites. The results of several hydrogen bonds, the radius of gyration, RMSF, RMSD, and free energy during the simulations showed good stability of ZINC1152745 with FoxM1 and Hsp70.
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Affiliation(s)
- Zahra Alimardan
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran,Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Maryam Abbasi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, I.R. Iran,Corresponding authors: M. Abbasi, Tel: +987633710406, Fax: +98- Gh.A. Khodarahmi, Tel: +98-3137927095, Fax: +98-3136680011
| | - Ghadamali Khodarahmi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran,Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran,Corresponding authors: M. Abbasi, Tel: +987633710406, Fax: +98- Gh.A. Khodarahmi, Tel: +98-3137927095, Fax: +98-3136680011
| | - Khosrow Kashfi
- Department of Molecular, Cellular, and Biomedical Sciences, Sophie Davis School of Biomedical Education, City University of New York School of Medicine, New York, USA,Graduate Program in Biology, City University of New York Graduate Center, New York, USA,Department of Chemistry and Physics, State University of New York at Old Westbury, New York, USA
| | - Farshid Hasanzadeh
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Aghaei Mahmud
- Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran,Department of Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
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38
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Marwa Abdullah Saleh, Karima Fadhil Ali, Basma M. Abd Razik. Synthesizing, Studying Molecular Docking, Characterizing, and Preliminary Evaluating Anti-Bacterial Effects of Derivatives of Serotonin Contain Imidazolidine Ring. AL MUSTANSIRIYAH JOURNAL OF PHARMACEUTICAL SCIENCES 2022; 22:1-16. [DOI: 10.32947/ajps.v22i3.884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
This study included synthesis of new serotonin derivatives in which imidazolidine rings are present in their structures. The final imidazolidine derivatives compounds were synthesized by reaction of synthesized
Schiff bases derivatives of serotonin with the glycine (NH2-CH2COOH) in presence of tetrahydrofuran (THF) as a solvent. The imidazolidine derivatives were identified by physical characteristics, FT-IR spectroscopy and 1H- NMR spectroscopy. Biological activities against two Gram negative (Klebsiella and E. coli) and two Gram positive (Streptococcus pyogenes and Staphylococcus aureus) bacteria were also distinguished. All the synthesized compounds III(a-d) exhibit moderate activities on four types of bacteria comparing with the activity of standard drug (Trimethoprim) but the highest activities of these compounds occur on Streptococcus pyogenes and their least activities occur on E. coli. The synthesized compounds were studied for the molecular docking to know the interaction and affinity of binding between them and bacteria
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39
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Yang J, Liu Y, Lan S, Yu S, Ma X, Luo D, Shan H, Zhong X, Yan G, Li R. Discovery of 2-Methyl-2-(4-(2-methyl-8-(1 H-pyrrolo[2,3- b]pyridin-6-yl)-1 H-naphtho[1,2- d]imidazol-1-yl)phenyl)propanenitrile as a Novel PI3K/mTOR Inhibitor with Enhanced Antitumor Efficacy In Vitro and In Vivo. J Med Chem 2022; 65:12781-12801. [PMID: 36191148 DOI: 10.1021/acs.jmedchem.2c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PI3K/Akt/mTOR signaling pathway is a validated drug target for cancer treatment that plays a critical role in controlling tumor growth, proliferation, and apoptosis. However, no FDA-approved PI3K/mTOR dual inhibitor exists. Thus, a candidate with a better curative effect and lower toxicity is still urgently needed. Herein, we design, synthesize, and evaluate compounds belonging to a novel series of 2-methyl-1H-imidazo[4,5-c]quinoline scaffold derivatives as PI3K/mTOR dual inhibitors. Among them, compound 8o was identified as a novel candidate with excellent kinase selectivity. It manifested remarkable antiproliferative activities against SW620 and HeLa cells. Western blot and immunohistochemical analysis results proved that 8o could regulate the PI3K/AKT/mTOR signaling pathway by inhibiting the phosphorylation of AKT and S6 proteins. Additionally, 8o presented a favorable pharmacokinetic property (oral bioavailability of 76.8%) and significant antitumor efficacy in vivo without obvious toxicity. Collectively, these results indicated that 8o is a promising agent for cancer treatment and merits further development.
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Affiliation(s)
- Jie Yang
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China.,Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu 610072, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yuanyuan Liu
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Suke Lan
- College of Chemistry & Environment Protection Engineering, Southwest Minzu University, Chengdu 610041, China
| | - Su Yu
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xinyu Ma
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Dan Luo
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Huifang Shan
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xinxin Zhong
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Guoyi Yan
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Rui Li
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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40
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Bhasin S, Nadar M, Hasija Y. Epicatechin analogues may hinder human parainfluenza virus infection by inhibition of hemagglutinin neuraminidase protein and prevention of cellular entry. J Mol Model 2022; 28:319. [DOI: 10.1007/s00894-022-05310-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 08/30/2022] [Indexed: 10/14/2022]
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41
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Williams-Noonan BJ, Speer MN, Le TC, Sadek MM, Thompson PE, Norton RS, Yuriev E, Barlow N, Chalmers DK, Yarovsky I. Membrane Permeating Macrocycles: Design Guidelines from Machine Learning. J Chem Inf Model 2022; 62:4605-4619. [PMID: 36178379 DOI: 10.1021/acs.jcim.2c00809] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to predict cell-permeable candidate molecules has great potential to assist drug discovery projects. Large molecules that lie beyond the Rule of Five (bRo5) are increasingly important as drug candidates and tool molecules for chemical biology. However, such large molecules usually do not cross cell membranes and cannot access intracellular targets or be developed as orally bioavailable drugs. Here, we describe a random forest (RF) machine learning model for the prediction of passive membrane permeation rates developed using a set of over 1000 bRo5 macrocyclic compounds. The model is based on easily calculated chemical features/descriptors as independent variables. Our random forest (RF) model substantially outperforms a multiple linear regression model based on the same features and achieves better performance metrics than previously reported models using the same underlying data. These features include: (1) polar surface area in water, (2) the octanol-water partitioning coefficient, (3) the number of hydrogen-bond donors, (4) the sum of the topological distances between nitrogen atoms, (5) the sum of the topological distances between nitrogen and oxygen atoms, and (6) the multiple molecular path count of order 2. The last three features represent molecular flexibility, the ability of the molecule to adopt different conformations in the aqueous and membrane interior phases, and the molecular "chameleonicity." Guided by the model, we propose design guidelines for membrane-permeating macrocycles. It is anticipated that this model will be useful in guiding the design of large, bioactive molecules for medicinal chemistry and chemical biology applications.
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Affiliation(s)
- Billy J Williams-Noonan
- School of Engineering, RMIT University, Melbourne3001, Australia.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Melissa N Speer
- University of Melbourne, Faculty of Engineering and Information Technology, Carlton3053, Australia
| | - Tu C Le
- School of Engineering, RMIT University, Melbourne3001, Australia
| | - Maiada M Sadek
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia.,ARC Centre for Fragment-Based Design, Monash University, Parkville, 3052, Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Nicholas Barlow
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne3001, Australia
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42
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Zetterberg FR, MacKinnon A, Brimert T, Gravelle L, Johnsson RE, Kahl-Knutson B, Leffler H, Nilsson UJ, Pedersen A, Peterson K, Roper JA, Schambye H, Slack RJ, Tantawi S. Discovery and Optimization of the First Highly Effective and Orally Available Galectin-3 Inhibitors for Treatment of Fibrotic Disease. J Med Chem 2022; 65:12626-12638. [PMID: 36154172 PMCID: PMC9574852 DOI: 10.1021/acs.jmedchem.2c00660] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Galectin-3 is a carbohydrate-binding protein central
to regulating
mechanisms of diseases such as fibrosis, cancer, metabolic, inflammatory,
and heart disease. We recently found a high affinity (nM) thiodigalactoside
GB0139 which currently is in clinical development (PhIIb) as an inhaled
treatment of idiopathic pulmonary fibrosis. To enable treatment of
systemically galectin-3 driven disease, we here present the first
series of selective galectin-3 inhibitors combining high affinity
(nM) with oral bioavailability. This was achieved by optimizing galectin-3
specificity and physical chemical parameters for a series of disubstituted
monogalactosides. Further characterization showed that this class
of compounds reduced profibrotic gene expression in liver myofibroblasts
and displayed antifibrotic activity in CCl4-induced liver
fibrosis and bleomycin-induced lung fibrosis mouse models. On the
basis of the overall pharmacokinetic, pharmacodynamic, and safety
profile, GB1211 was selected as the clinical candidate and is currently
in phase IIa clinical trials as a potential therapy for liver cirrhosis
and cancer.
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Affiliation(s)
- Fredrik R Zetterberg
- Galecto Biotech AB, Sahlgrenska Science Park, Medicinaregatan 8 A, SE-413 46 Gothenburg, Sweden
| | - Alison MacKinnon
- Galecto Biotech ApS, Nine Edinburgh Bioquarter, 9 Little France Road, Edinburgh EH16 4UX, U.K
| | - Thomas Brimert
- Red Glead Discovery AB, Medicon Village, SE-223 63 Lund, Sweden.,Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Lise Gravelle
- Galecto Biotech ApS, Cobis Science Park, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark
| | | | - Barbro Kahl-Knutson
- Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Hakon Leffler
- Department of Laboratory Medicine, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Ulf J Nilsson
- Galecto Biotech AB, Sahlgrenska Science Park, Medicinaregatan 8 A, SE-413 46 Gothenburg, Sweden.,Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Anders Pedersen
- Galecto Biotech ApS, Cobis Science Park, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark
| | - Kristoffer Peterson
- Galecto Biotech AB, Sahlgrenska Science Park, Medicinaregatan 8 A, SE-413 46 Gothenburg, Sweden.,Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - James A Roper
- Galecto Biotech ApS, Stevenage Bioscience Catalyst, Stevenage, SG1 2FX Hertfordshire, U.K
| | - Hans Schambye
- Galecto Biotech ApS, Cobis Science Park, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark
| | - Robert J Slack
- Galecto Biotech ApS, Stevenage Bioscience Catalyst, Stevenage, SG1 2FX Hertfordshire, U.K
| | - Susan Tantawi
- Galecto Biotech ApS, Cobis Science Park, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark
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43
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Argikar U, Blatter M, Bednarczyk D, Chen Z, Cho YS, Doré M, Dumouchel JL, Ho S, Hoegenauer K, Kawanami T, Mathieu S, Meredith E, Möbitz H, Murphy SK, Parthasarathy S, Soldermann CP, Santos J, Silver S, Skolnik S, Stojanovic A. Paradoxical Increase of Permeability and Lipophilicity with the Increasing Topological Polar Surface Area within a Series of PRMT5 Inhibitors. J Med Chem 2022; 65:12386-12402. [PMID: 36069672 DOI: 10.1021/acs.jmedchem.2c01068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An imidazolone → triazolone replacement addressed the limited passive permeability of a series of protein arginine methyl transferase 5 (PRMT5) inhibitors. This increase in passive permeability was unexpected given the increase in the hydrogen bond acceptor (HBA) count and topological polar surface area (TPSA), two descriptors that are typically inversely correlated with permeability. Quantum mechanics (QM) calculations revealed that this unusual effect was due to an electronically driven disconnect between TPSA and 3D-PSA, which manifests in a reduction in overall HBA strength as indicated by the HBA moment descriptor from COSMO-RS (conductor-like screening model for real solvation). HBA moment was subsequently deployed as a design parameter leading to the discovery of inhibitors with not only improved passive permeability but also reduced P-glycoprotein (P-gp) transport. Our case study suggests that hidden polarity as quantified by TPSA-3DPSA can be rationally designed through QM calculations.
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Affiliation(s)
- Upendra Argikar
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Blatter
- Novartis Institutes for BioMedical Research, Basel 4002, Switzerland
| | - Dallas Bednarczyk
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Zhuoliang Chen
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Young Shin Cho
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Michaël Doré
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Jennifer L Dumouchel
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Samuel Ho
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | | | - Toshio Kawanami
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Simon Mathieu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Erik Meredith
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Henrik Möbitz
- Novartis Institutes for BioMedical Research, Basel 4002, Switzerland
| | - Stephen K Murphy
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | | | | | - Jobette Santos
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Serena Silver
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Suzanne Skolnik
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
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44
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Mohamed EAR, Abdelwahab SF, Alqaisi AM, Nasr AMS, Hassan HA. Identification of promising anti-EBOV inhibitors: de novo drug design, molecular docking and molecular dynamics studies. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220369. [PMID: 36177201 PMCID: PMC9515638 DOI: 10.1098/rsos.220369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
The Ebola virus (EBOV) outbreak was recorded as the largest in history and caused many fatalities. As seen in previous studies, drug repurposing and database filtration were the two major pathways to searching for potent compounds against EBOV. In this study, a deep learning (DL) approach via the LigDream tool was employed to obtain novel and effective anti-EBOV inhibitors. Based on the galidesivir (BCX4430) chemical structure, 100 compounds were collected and inspected using various in silico approaches. Results from the molecular docking study indicated that mol1_069 and mol1_092 were the best two potent compounds with a docking score of -7.1 kcal mol-1 and -7.0 kcal mol-1, respectively. Molecular dynamics simulations, in addition to binding energy calculations, were conducted over 100 ns. Both compounds exhibited lower binding energies than BCX4430. Furthermore, compared with BCX4430 (%Absorption = 60.6%), mol1_069 and mol1_092 scored higher values of % Absorption equal to 68.1% and 63.7%, respectively. The current data point to the importance of using DL in the drug design process instead of conventional methods such as drug repurposing or database filtration. In conclusion, mol1_069 and mol1_092 are promising anti-EBOV drug candidates that require further in vitro and in vivo investigations.
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Affiliation(s)
- Eslam A. R. Mohamed
- Department of Chemistry, Faculty of Science, Minia University, Minia 61511, Egypt
| | - Sayed F. Abdelwahab
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, PO Box 11099, Taif 21944, Saudi Arabia
| | | | | | - Heba Ali Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Sohag University, Sohag 82524, Egypt
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45
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Pro-Apoptotic Antitumoral Effect of Novel Acridine-Core Naphthoquinone Compounds against Oral Squamous Cell Carcinoma. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165148. [PMID: 36014389 PMCID: PMC9415509 DOI: 10.3390/molecules27165148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/03/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022]
Abstract
Oral squamous cell carcinoma (OSCC) is a global public health problem with high incidence and mortality. The chemotherapeutic agents used in the clinic, alone or in combination, usually lead to important side effects. Thus, the discovery and development of new antineoplastic drugs are essential to improve disease prognosis and reduce toxicity. In the present study, acridine-core naphthoquinone compounds were synthesized and evaluated for their antitumor activity in OSCC cells. The mechanism of action, pharmacokinetics, and toxicity parameters of the most promising compound was further analyzed using in silico, in vitro, and in vivo methods. Among the derivatives, compound 4e was highly cytotoxic (29.99 µM) and selective (SI 2.9) at levels comparable and generally superior to chemotherapeutic controls. Besides, compound 4e proved to be non-hemolytic, stable, and well tolerated in animals at all doses tested. Mechanistically, compound 4e promoted cell death by apoptosis in the OSCC cell, and molecular docking studies suggested this compound possibly targets enzymes important for tumor progression, such as RSK2, PKM2, and topoisomerase IIα. Importantly, compound 4e presented a pharmacological profile within desirable parameters for drug development, showing promise for future preclinical trials.
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46
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Ushiki Y, Kawabe K, Yamamoto-Okada K, Uneuchi F, Asanuma Y, Yamaguchi C, Ohta H, Shibata T, Abe T, Okumura-Kitajima L, Kosai Y, Endo M, Otake K, Munetomo E, Takahashi T, Kakinuma H. Design, synthesis and biological evaluation of novel indole derivatives as gut-selective NaPi2b inhibitors. Bioorg Med Chem 2022; 66:116783. [PMID: 35576656 DOI: 10.1016/j.bmc.2022.116783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 11/02/2022]
Abstract
Intestinal sodium-dependent phosphate transport protein 2b (SLC34A2, NaPi2b) inhibitors are expected to be potential new candidates for anti-hyperphosphatemia drugs. However, a risk of on-target side effects based on the inhibition of NaPi2b in the lung and testis has been reported.In this article, we report on our identification of novel indole derivatives as gut-selective NaPi2b inhibitors with good activity, low systemic exposure and moderate hydrophobicity.In particular, gut-selective compound 27, with even lower bioavailability and lower systemic exposure as compared to previously reported pyridine derivatives, demonstrated excellent phosphate absorption-inhibitory effect in SD rats. Compound 27 has an ideal profile and appears to offer promise as a candidate drug for the treatment of hyperphosphatemia, with minimal risk of side effects due to systemic exposure.
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Affiliation(s)
- Yasunobu Ushiki
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan.
| | - Kenichi Kawabe
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Kumiko Yamamoto-Okada
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Fumito Uneuchi
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Yuta Asanuma
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Chitose Yamaguchi
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Hiroshi Ohta
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Tsuyoshi Shibata
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Tomohiro Abe
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Lisa Okumura-Kitajima
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Yuki Kosai
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Mayumi Endo
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Katsumasa Otake
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Eiji Munetomo
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Teisuke Takahashi
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
| | - Hiroyuki Kakinuma
- Taisho Pharmaceutical Co., Ltd., 1-403 Yoshino-cho, Kita-ku, Saitama 331-9530, Japan
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Integration of Ligand-Based and Structure-Based Methods for the Design of Small-Molecule TLR7 Antagonists. Molecules 2022; 27:molecules27134026. [PMID: 35807273 PMCID: PMC9268101 DOI: 10.3390/molecules27134026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 12/30/2022] Open
Abstract
Toll-like receptor 7 (TLR7) is activated in response to the binding of single-stranded RNA. Its over-activation has been implicated in several autoimmune disorders, and thus, it is an established therapeutic target in such circumstances. TLR7 small-molecule antagonists are not yet available for therapeutic use. We conducted a ligand-based drug design of new TLR7 antagonists through a concerted effort encompassing 2D-QSAR, 3D-QSAR, and pharmacophore modelling of 54 reported TLR7 antagonists. The developed 2D-QSAR model depicted an excellent correlation coefficient (R2training: 0.86 and R2test: 0.78) between the experimental and estimated activities. The ligand-based drug design approach utilizing the 3D-QSAR model (R2training: 0.95 and R2test: 0.84) demonstrated a significant contribution of electrostatic potential and steric fields towards the TLR7 antagonism. This consolidated approach, along with a pharmacophore model with high correlation (Rtraining: 0.94 and Rtest: 0.92), was used to design quinazoline-core-based hTLR7 antagonists. Subsequently, the newly designed molecules were subjected to molecular docking onto the previously proposed binding model and a molecular dynamics study for a better understanding of their binding pattern. The toxicity profiles and drug-likeness characteristics of the designed compounds were evaluated with in silico ADMET predictions. This ligand-based study contributes towards a better understanding of lead optimization and the future development of potent TLR7 antagonists.
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Koca M, Güller U, Güller P, Dağalan Z, Nişancı B. Design and Synthesis of Novel Dual Cholinesterase Inhibitors: In Vitro Inhibition Studies Supported with Molecular Docking. Chem Biodivers 2022; 19:e202200015. [PMID: 35470963 DOI: 10.1002/cbdv.202200015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/11/2022] [Indexed: 11/05/2022]
Abstract
The major cholinesterase enzymes, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), are important in the therapy of Alzheimer's disease (AD) based on the cholinergic hypothesis. As a result, in recent years, the investigation of dual cholinesterase inhibition methods has become important among scientists. In this study, novel N-(4-chlorobenzyl)-3,4-dimethoxy-N-(m-substituted)benzamide derivatives were synthesized. Then, inhibitory properties of these derivatives were examined in human AChE and BuChE in vitro and possible interactions were determined by molecular docking studies. All benzamide derivatives were exhibited dual inhibitory character and high BBB permeability. The most effective inhibitor was found as N7 for both AChE and BuChE with IC50 values of 1.57 and 2.85 μM, respectively. Besides the most potent inhibitor was predicted as N7 in terms of binding energies with -12.18 kcal/mol and -9.92 kcal/mol, respectively. The reason for these results is that bromine (N7) is the bulkiest molecule among the other substituted groups. These derivatives could be exploited to develop new medications for the treatment of central nervous system-related diseases as AD by acting as dual inhibitors of AChE and BChE.
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Affiliation(s)
- Mehmet Koca
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Atatürk University, Erzurum, Turkey
| | - Uğur Güller
- Department of Food Engineering, Faculty of Engineering, Iğdır University, Iğdır, Turkey
| | - Pınar Güller
- Department of Chemistry, Faculty of Sciences, Atatürk University, Erzurum, Turkey
| | - Ziya Dağalan
- Department of Chemistry, Faculty of Sciences, Atatürk University, Erzurum, Turkey
| | - Bilal Nişancı
- Department of Chemistry, Faculty of Sciences, Atatürk University, Erzurum, Turkey
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Abstract
Peptides have traditionally been perceived as poor drug candidates due to unfavorable characteristics mainly regarding their pharmacokinetic behavior, including plasma stability, membrane permeability and circulation half-life. Nonetheless, in recent years, general strategies to tackle those shortcomings have been established, and peptides are subsequently gaining increasing interest as drugs due to their unique ability to combine the advantages of antibodies and small molecules. Macrocyclic peptides are a special focus of drug development efforts due to their ability to address so called ‘undruggable’ targets characterized by large and flat protein surfaces lacking binding pockets. Here, the main strategies developed to date for adapting peptides for clinical use are summarized, which may soon help usher in an age highly shaped by peptide-based therapeutics. Nonetheless, limited membrane permeability is still to overcome before peptide therapeutics will be broadly accepted.
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