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Thapliyal S, Vishnoi R, Murti Y, Kumar R, Chavan N, Rawat P, Joshi G, Dwivedi AR, Goel KK. Exploring anticancer properties of the phytoconstituents and comparative analysis of their chemical space parameters with USFDA-approved synthetic anticancer agents. Chem Biol Drug Des 2024; 103:e14561. [PMID: 38862268 DOI: 10.1111/cbdd.14561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/30/2024] [Accepted: 05/22/2024] [Indexed: 06/13/2024]
Abstract
The present review article thoroughly analyses natural products and their derived phytoconstituents as a rich source of plausible anticancer drugs. The study thoroughly explores the chemical components derived from various natural sources, thus emphasizing their unique structural characteristics and therapeutic potential as an anticancer agent. The review contains the critical chemical constituents' in-depth molecular mechanisms, their source's chemical structures and the categories. The review also comprises an exhaustive and comprehensive analysis of different chemical spacing parameters of the anticancer agents derived from natural products. It compares them with USFDA-approved synthetic anticancer drugs up to 2020, thus providing a meaningful understanding of the relationship between natural and synthetic compounds portraying the anticancer assets. The review also delves more deeply into the chemical analysis of the heterocyclic moieties from the natural product arena, illustrating the anticancer mechanisms. The present article is, therefore, expected to serve as a valuable resource for natural product and medicinal chemists, encouraging and promoting an integrated approach to exploit the potential of natural products in drug discovery development and translational research, which have a prerequisite of bench to bedside approach. The work could guide researchers toward innovative approaches for the ever-evolving field of anticancer drug discovery.
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Affiliation(s)
- Somesh Thapliyal
- Department of Pharmaceutical Sciences, Hemvati Nandan Bahuguna Garhwal University (Central University), Srinagar, India
| | - Ritu Vishnoi
- Department of Botany, Hariom Saraswati PG College, Dhanauri, Haridwar, Uttarakhand, India
| | - Yogesh Murti
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India
| | - Roshan Kumar
- Department of Microbiology, Central University of Punjab, Ghudda, Bathinda, India
| | - Nirja Chavan
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Pramod Rawat
- Graphic Era (Deemed to be University) Clement Town Dehradun, Dehradun, India
- Graphic Era Hill University Clement Town Dehradun, Dehradun, India
| | - Gaurav Joshi
- Department of Pharmaceutical Sciences, Hemvati Nandan Bahuguna Garhwal University (Central University), Srinagar, India
| | - Ashish Ranjan Dwivedi
- Department of Medicinal Chemistry, GITAM School of Pharmacy, GITAM (Deemed to be) University, Hyderabad, India
| | - Kapil Kumar Goel
- Department of Pharmaceutical Sciences, Gurukul Kangri (Deemed to Be University), Haridwar, Uttarakhand, India
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Kaboudi N, Asl SG, Nourani N, Shayanfar A. Solubilization of drugs using beta-cyclodextrin: Experimental data and modeling. ANNALES PHARMACEUTIQUES FRANÇAISES 2024; 82:663-672. [PMID: 38340807 DOI: 10.1016/j.pharma.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Many drug candidates fail to complete the entire drug development process because of poor physicochemical properties. Solubility is an important physicochemical property which plays a vital role in various stages of drug discovery and development. Several methods have been proposed to enhance the solubility of drugs, and complex formation with cyclodextrins is among them. Beta-cyclodextrin (βCD) is a common excipient for solubilization of drugs. The aim of this study is to develop the mechanistic QSPR models to predict the solubility enhancement of a drug in the presence of βCD. In this study, the solubility enhancement of some drugs in the presence of 10mM βCD at 25°C was experimentally determined or collected from the literature. Two different models to predict the solubilization by βCD were developed by binary logistic regression using structural properties of drugs with more than 80% accuracy. Polar surface area and excess molar refraction are the main parameters for estimating solubilization by βCD. Moreover, other descriptors related to hydrophobicity and the capability of hydrogen bonding formation of molecules could improve the accuracy of the established models.
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Affiliation(s)
- Navid Kaboudi
- Student Research Committee, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saba Ghasemi Asl
- Student Research Committee, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasim Nourani
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Shayanfar
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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3
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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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4
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Mehta V, Dwivedi AR, Ludhiadch A, Rana V, Goel KK, Uniyal P, Joshi G, Kumar A, Kumar B. A decade of USFDA-approved small molecules as anti-inflammatory agents: Recent trends and Commentaries on the "industrial" perspective. Eur J Med Chem 2024; 263:115942. [PMID: 38000212 DOI: 10.1016/j.ejmech.2023.115942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/05/2023] [Accepted: 11/05/2023] [Indexed: 11/26/2023]
Abstract
Inflammation is the human body's defence process against various pathogens, toxic substances, irradiation, and physically injured cells that have been damaged. Inflammation is characterized by swelling, pain, redness, heat, as well as diminished tissue function. Multiple important inflammatory markers determine the prognosis of inflammatory processes, which include likes of pro-inflammatory cytokines which are controlled by nuclear factor kappa-B (NF-kB), mitogen-activated protein kinase (MAPK), Janus kinase signal transducer and activator of transcription (JAK-STAT) pathway, all of which are activated in response to the stimulation of specific receptors. Besides these, the cyclooxygenase (COX) enzyme family also plays a significant role in inflammation. The current review is kept forth to compile a summary of small molecules-based drugs approved by the USFDA during the study period of 2013-2023. A thorough discussion has also been made to focus on biologics, macromolecules, and small chemical entities approved during this study period and their greener synthetic routes with a brief discussion on the chemical spacing parameters of anti-inflammatory drugs. The compilation is expected to assist the medicinal chemist and the scientist actively engaged in drug discovery and development of anti-inflammatory agents from newer perspectives during the current years.
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Affiliation(s)
- Vikrant Mehta
- Department of Cell Systems & Anatomy, University of Texas Health Science Center at San Antonio, Texas, 78229, USA
| | | | - Abhilash Ludhiadch
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, 10032, USA
| | - Vikas Rana
- School of Pharmacy, Graphic Era Hill University, Clement town, Dehradun, 248002, Uttarakhand, India
| | - Kapil Kumar Goel
- Department of Pharmaceutical Sciences, Gurukul Kangri (Deemed to Be University), Haridwar, 249404, Uttarakhand, India
| | - Prerna Uniyal
- School of Pharmacy, Graphic Era Hill University, Clement town, Dehradun, 248002, Uttarakhand, India
| | - Gaurav Joshi
- Department of Pharmaceutical Sciences, HNB Garhwal University, Chauras Campus, Garhwal, Srinagar, Uttarakhand, 246174, India; Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, 248002, Uttarakhand, India.
| | - Asim Kumar
- Amity Institute of Pharmacy (AIP), Amity University Haryana, Panchgaon, Manesar, 122413, India.
| | - Bhupinder Kumar
- Department of Pharmaceutical Sciences, HNB Garhwal University, Chauras Campus, Garhwal, Srinagar, Uttarakhand, 246174, India.
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Mitra D, Paul M, Thatoi H, Das Mohapatra PK. Potentiality of bioactive compounds as inhibitor of M protein and F protein function of human respiratory syncytial virus. In Silico Pharmacol 2023; 12:5. [PMID: 38148755 PMCID: PMC10749291 DOI: 10.1007/s40203-023-00178-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/03/2023] [Indexed: 12/28/2023] Open
Abstract
The human respiratory syncytial virus (RSV) creates a pandemic every year in several countries in the world. Lack of target therapeutics and absence of vaccines have prompted scientists to create novel vaccines or small chemical treatments against RSV's numerous targets. The matrix (M) protein and fusion (F) glycoprotein of RSV are well characterized and attractive drug targets. Five bioactive compounds from Alnus japonica (Thunb.) Steud. were taken into consideration as lead compounds. Drug-likeness characters of them showed the drugs are non-toxic and non-mutagenic and mostly lipophobic. Molecular docking reveals that all bioactive compounds have better binding and better inhibitory effect than ribavirin which is currently used against RSV. Praecoxin A appeared as the best lead compound between them. It creates 7 different types of bonds with amino acids of M protein and 5 different types of bonds with amino acids of F protein. Van der Waals interactions highly influenced the binding energies. Molecular dynamic simulations represent the non-deviated and less fluctuating nature of praecoxin A. Principal Component Analysis showed praecoxin A complex with RSV matrix protein is more stable than ribavirin complex. This study will help to develop a new drug to inhibit RSV. All ligands were minimized through semi-empirical PM3 process with MOPAC. Toxicity was tested by ProTox-II server. Molecular docking studies were carried out using AutoDock 4.2. Molecular dynamics simulations for 100 ns were carried out through GROMACS 5.12 MD and GROMOS96 43a1 force field. The graphs were produced by GROMACS's XMGrace program. Graphical abstract
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Affiliation(s)
- Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, West Bengal 733134 India
| | - Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, Odisha 757003 India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, Odisha 757003 India
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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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Wijesinghe TP, Kaya B, Gonzálvez MA, Harmer JR, Gholam Azad M, Bernhardt PV, Dharmasivam M, Richardson DR. Steric Blockade of Oxy-Myoglobin Oxidation by Thiosemicarbazones: Structure-Activity Relationships of the Novel PPP4pT Series. J Med Chem 2023; 66:15453-15476. [PMID: 37922410 DOI: 10.1021/acs.jmedchem.3c01612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
The di-2-pyridylketone thiosemicarbazones demonstrated marked anticancer efficacy, prompting progression of DpC to clinical trials. However, DpC induced deleterious oxy-myoglobin oxidation, stifling development. To address this, novel substituted phenyl thiosemicarbazone (PPP4pT) analogues and their Fe(III), Cu(II), and Zn(II) complexes were prepared. The PPP4pT analogues demonstrated potent antiproliferative activity (IC50: 0.009-0.066 μM), with the 1:1 Cu:L complexes showing the greatest efficacy. Substitutions leading to decreased redox potential of the PPP4pT:Cu(II) complexes were associated with higher antiproliferative activity, while increasing potential correlated with increased redox activity. Surprisingly, there was no correlation between redox activity and antiproliferative efficacy. The PPP4pT:Fe(III) complexes attenuated oxy-myoglobin oxidation significantly more than the clinically trialed thiosemicarbazones, Triapine, COTI-2, and DpC, or earlier thiosemicarbazone series. Incorporation of phenyl- and styryl-substituents led to steric blockade, preventing approach of the PPP4pT:Fe(III) complexes to the heme plane and its oxidation. The 1:1 Cu(II):PPP4pT complexes were inert to transmetalation and did not induce oxy-myoglobin oxidation.
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Affiliation(s)
- Tharushi P Wijesinghe
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane 4111, Australia
| | - Busra Kaya
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane 4111, Australia
| | - Miguel A Gonzálvez
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, University of Queensland, Brisbane 4072, Australia
| | - Mahan Gholam Azad
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane 4111, Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
| | - Mahendiran Dharmasivam
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane 4111, Australia
| | - Des R Richardson
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane 4111, Australia
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
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8
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Akash S, Bibi S, Biswas P, Mukerjee N, Khan DA, Hasan MN, Sultana NA, Hosen ME, Jardan YAB, Nafidi HA, Bourhia M. Revolutionizing anti-cancer drug discovery against breast cancer and lung cancer by modification of natural genistein: an advanced computational and drug design approach. Front Oncol 2023; 13:1228865. [PMID: 37817764 PMCID: PMC10561655 DOI: 10.3389/fonc.2023.1228865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/15/2023] [Indexed: 10/12/2023] Open
Abstract
Breast and lung cancer are two of the most lethal forms of cancer, responsible for a disproportionately high number of deaths worldwide. Both doctors and cancer patients express alarm about the rising incidence of the disease globally. Although targeted treatment has achieved enormous advancements, it is not without its drawbacks. Numerous medicines and chemotherapeutic drugs have been authorized by the FDA; nevertheless, they can be quite costly and often fall short of completely curing the condition. Therefore, this investigation has been conducted to identify a potential medication against breast and lung cancer through structural modification of genistein. Genistein is the active compound in Glycyrrhiza glabra (licorice), and it exhibits solid anticancer efficiency against various cancers, including breast cancer, lung cancer, and brain cancer. Hence, the design of its analogs with the interchange of five functional groups-COOH, NH2 and OCH3, Benzene, and NH-CH2-CH2-OH-have been employed to enhance affinities compared to primary genistein. Additionally, advanced computational studies such as PASS prediction, molecular docking, ADMET, and molecular dynamics simulation were conducted. Firstly, the PASS prediction spectrum was analyzed, revealing that the designed genistein analogs exhibit improved antineoplastic activity. In the prediction data, breast and lung cancer were selected as primary targets. Subsequently, other computational investigations were gradually conducted. The mentioned compounds have shown acceptable results for in silico ADME, AMES toxicity, and hepatotoxicity estimations, which are fundamental for their oral medication. It is noteworthy that the initial binding affinity was only -8.7 kcal/mol against the breast cancer targeted protein (PDB ID: 3HB5). However, after the modification of the functional group, when calculating the binding affinities, it becomes apparent that the binding affinities increase gradually, reaching a maximum of -11.0 and -10.0 kcal/mol. Similarly, the initial binding affinity was only -8.0 kcal/mol against lung cancer (PDB ID: 2P85), but after the addition of binding affinity, it reached -9.5 kcal/mol. Finally, a molecular dynamics simulation was conducted to study the molecular models over 100 ns and examine the stability of the docked complexes. The results indicate that the selected complexes remain highly stable throughout the 100-ns molecular dynamics simulation runs, displaying strong correlations with the binding of targeted ligands within the active site of the selected protein. It is important to further investigate and proceed to clinical or wet lab experiments to determine the practical value of the proposed compounds.
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Affiliation(s)
- Shopnil Akash
- Faculty of Allied Health Science, Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Partha Biswas
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Kolkata, India
| | - Dhrubo Ahmed Khan
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Nazmul Hasan
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Nazneen Ahmeda Sultana
- Faculty of Allied Health Science, Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Md. Eram Hosen
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Yousef A. Bin Jardan
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | - Hiba-Allah Nafidi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Laboratory of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
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Bhowmik P, Baezid HM, Arabi II. Assessment of antidiabetic activity of three Phenylspirodrimanes from fungus Stachybotrys chartarum MUT 3308 by ADME, QSAR, molecular docking and molecular dynamics simulation studies against protein tyrosine phosphatase 1B (PTP1B). J Biomol Struct Dyn 2023:1-15. [PMID: 37698508 DOI: 10.1080/07391102.2023.2256410] [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: 05/29/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023]
Abstract
Phenylspirodrimanes (PSD) are the sesquiterpene quinone type meroterpenoids found in nature. PSDs are found to exhibit inhibitory activity against immunocomplex diseases, and tyrosine kinase receptors. Three of the different PSDs C1, C2, and C3 that have been reported to be isolated from the sponge-associated fungus Stachybotrys chartarum MUT 3308 are selected for studying their possible inhibitory effect against type 2 diabetes mellitus. Mechanistically, blocking protein tyrosine phosphatase 1B (PTP1B) helps to reduce the insulin resistance induction caused by the high expression of PTP1B. The QSAR, ADME, toxicity (T) study was carried out to predict the pharmacokinetic properties and the biological activities of the PSDs. PASS prediction web tool was used to find and select the target proteins 1NNY, and 2HNP. According to the molecular docking simulations, C1 and C2 showed better binding affinity of -8.5 kcal/mol, and -8.1 kcal/mol respectively against 1NNY compared to the control ligand. RMSD, RMSF, Rg, and SASA analysis revealed that both C1, and C2 showed better stability, minor conformational changes, and minor fluctuation upon binding to PTP1B. Protein contact analysis was carried out to validate the residues that are in contact with the ligands according to molecular docking studies. Overall, C1, and C2 could be proposed as novel natural hits to be developed and small modifications of these PSDs could result in inducing the binding affinity significantly, although experimental validation is required for further evaluation of the work.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prasenjit Bhowmik
- Department of Chemistry-BMC, Biochemistry, Disciplinary Domain of Science and Technology, Uppsala University, Uppsala, Sweden
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
- Department of Textile Engineering, Green University of Bangladesh, Narayanganj, Bangladesh
| | - Hossain Mohammad Baezid
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Ishmam Ibnul Arabi
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
- Department of Textile Engineering, Green University of Bangladesh, Narayanganj, Bangladesh
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10
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Gandla K, Islam F, Zehravi M, Karunakaran A, Sharma I, Haque MA, Kumar S, Pratyush K, Dhawale SA, Nainu F, Khan SL, Islam MR, Al-Mugren KS, Siddiqui FA, Emran TB, Khandaker MU. Natural polymers as potential P-glycoprotein inhibitors: Pre-ADMET profile and computational analysis as a proof of concept to fight multidrug resistance in cancer. Heliyon 2023; 9:e19454. [PMID: 37662819 PMCID: PMC10472248 DOI: 10.1016/j.heliyon.2023.e19454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023] Open
Abstract
P-glycoprotein (P-gp) is known as the "multidrug resistance protein" because it contributes to tumor resistance to several different classes of anticancer drugs. The effectiveness of such polymers in treating cancer and delivering drugs has been shown in a wide range of in vitro and in vivo experiments. The primary objective of the present study was to investigate the inhibitory effects of several naturally occurring polymers on P-gp efflux, as it is known that P-gp inhibition can impede the elimination of medications. The objective of our study is to identify polymers that possess the potential to inhibit P-gp, a protein involved in drug resistance, with the aim of enhancing the effectiveness of anticancer drug formulations. The ADMET profile of all the selected polymers (Agarose, Alginate, Carrageenan, Cyclodextrin, Dextran, Hyaluronic acid, and Polysialic acid) has been studied, and binding affinities were investigated through a computational approach using the recently released crystal structure of P-gp with PDB ID: 7O9W. The advanced computational study was also done with the help of molecular dynamics simulation. The aim of the present study is to overcome MDR resulting from the activity of P-gp by using such polymers that can inhibit P-gp when used in formulations. The docking scores of native ligand, Agarose, Alginate, Carrageenan, Chitosan, Cyclodextrin, Dextran, Hyaluronic acid, and Polysialic acid were found to be -10.7, -8.5, -6.6, -8.7, -8.6, -24.5, -6.7, -8.3, and -7.9, respectively. It was observed that, Cyclodextrin possess multiple properties in drug delivery science and here also demonstrated excellent binding affinity. We propose that drug efflux-related MDR may be prevented by the use of Agarose, Carregeenan, Chitosan, Cyclodextrin, Hyaluronic acid, and/or Polysialic acid in the administration of anticancer drugs.
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Affiliation(s)
- Kumaraswamy Gandla
- Department of Pharmaceutical Analysis, Chaitanya (Deemed to be University), Himayath Nagar, Hyderabad 500075, Telangana, India
| | - Fahadul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Mehrukh Zehravi
- Department of Clinical Pharmacy Girls Section, Prince Sattam Bin Abdul Aziz University, Al-Kharj 11942, Saudi Arabia
| | - Anandakumar Karunakaran
- Department of Pharmaceutical Analysis, Vivekanandha Pharmacy College for Women, Beerachipalayam, Sankari West, Sankari, Salem, Tamil Nadu, - 637 303, India
| | - Indu Sharma
- Department of Physics, Career Point University, Hamirpur, Himachal Pradesh 176041, India
| | - M. Akiful Haque
- Department of Pharmaceutical Analysis, School of Pharmacy, Anurag University, Hyderabad, India
| | - Sanjay Kumar
- Department of Pharmacognosy, Laureate Institute of Pharmacy, VPO Kathog, Dehra, Kangra, Himachal Pradesh 176031, India
| | - Kumar Pratyush
- Department of Pharmaceutical Chemistry, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule, Maharashtra, 424001, India
| | - Sachin A. Dhawale
- Shreeyash Institute of Pharmaceutical Education and Research Aurangabad, 431 005, Maharashtra, India
| | - Firzan Nainu
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Sharuk L. Khan
- Department of Pharmaceutical Chemistry, N.B.S. Institute of Pharmacy, Ausa 413520, Maharashtra, India
- Department of Pharmaceutical Chemistry, School of Pharmacy, Anurag University, Hyderabad, India
| | - Md Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Kholoud Saad Al-Mugren
- Department of Physics, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428 Riyadh 11671, Saudi Arabia
| | - Falak A. Siddiqui
- Department of Pharmaceutical Chemistry, N.B.S. Institute of Pharmacy, Ausa 413520, Maharashtra, India
- Department of Pharmaceutical Chemistry, School of Pharmacy, Anurag University, Hyderabad, India
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Mayeen Uddin Khandaker
- Centre for Applied Physics and Radiation Technologies, School of Engineering and Technology, Sunway University, Bandar Sunway 47500, Selangor, Malaysia
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11
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Kumar A, Kalra S, Jangid K, Jaitak V. Flavonoids as P-glycoprotein inhibitors for multidrug resistance in cancer: an in-silico approach. J Biomol Struct Dyn 2023; 41:7627-7639. [PMID: 36120941 DOI: 10.1080/07391102.2022.2123390] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
Cancer has become a leading cause of mortality due to non-communicable diseases after cardiovascular disease worldwide and is increasing day by day at a daunting pace. According to an estimate by 2040 there will be 28.4 million cancer cases. Occurrence of multidrug resistance has further worsened the scenario of available cancer treatment. Among different mechanisms of multidrug resistance efflux of xenobiotics by ABC transporter is of prime importance. P-glycoprotein (P-gp) is the major factor behind occurrence of multidrug resistance due to its wide distribution and invariably big binding cavity. Various generations of chemical inhibitors for P-gp have been designed and tested are not devoid of major side effects. Thus, in present study flavonoids a major class of natural compounds was virtually screened in order to find molecules which can be used as selective P-gp inhibitors to be used along with chemotherapeutics. After screening 4275 molecules from different classes of flavonoids i.e. flavan, flavanol, flavonone, flavone, anthocyanins, and isoflavone, through Glide docking top ten hit molecules were selected based on their binding affinity, binding energy calculation and pharmacokinetic properties. All the hit molecules were found to have docking score within the range of -11.202 to -9.699 kcal/mol showing very strong interaction with the amino acid residues of binding pocket. Whereas, dock score of standard P-gp inhibitor verapamil was -4.984 kcal/mol. The ligand and protein complex were found to be quite stable while run through molecular dynamics simulations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amit Kumar
- Laboratory of Natural Product Chemistry, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
| | - Sourav Kalra
- School of Pharmacy, Chitkara University, Baddi, Himachal Pradesh, India
| | - Kailash Jangid
- Department of Pharmacy, School of Chemical Sciences & Pharmacy, Central University of Rajasthan, Ajmer, India
| | - Vikas Jaitak
- Laboratory of Natural Product Chemistry, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
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12
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Aguila-Muñoz DG, Vázquez-Lira G, Sarmiento-Tlale E, Cruz-López MC, Jiménez-Montejo FE, López Y López VE, Escalante CH, Andrade-Pavón D, Gómez-García O, Tamariz J, Mendieta-Moctezuma A. Synthesis and Molecular Docking Studies of Alkoxy- and Imidazole-Substituted Xanthones as α-Amylase and α-Glucosidase Inhibitors. Molecules 2023; 28:molecules28104180. [PMID: 37241920 DOI: 10.3390/molecules28104180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Current antidiabetic drugs have severe side effects, which may be minimized by new selective molecules that strongly inhibit α-glucosidase and weakly inhibit α-amylase. We have synthesized novel alkoxy-substituted xanthones and imidazole-substituted xanthones and have evaluated them for their in silico and in vitro α-glucosidase and α-amylase inhibition activity. Compounds 6c, 6e, and 9b promoted higher α-glucosidase inhibition (IC50 = 16.0, 12.8, and 4.0 µM, respectively) and lower α-amylase inhibition (IC50 = 76.7, 68.1, and >200 µM, respectively) compared to acarbose (IC50 = 306.7 µM for α-glucosidase and 20.0 µM for α-amylase). Contrarily, derivatives 10c and 10f showed higher α-amylase inhibition (IC50 = 5.4 and 8.7 µM, respectively) and lower α-glucosidase inhibition (IC50 = 232.7 and 145.2 µM, respectively). According to the structure-activity relationship, attaching 4-bromobutoxy or 4'-chlorophenylacetophenone moieties to the 2-hydroxy group of xanthone provides higher α-glucosidase inhibition and lower α-amylase inhibition. In silico studies suggest that these scaffolds are key in the activity and interaction of xanthone derivatives. Enzymatic kinetics studies showed that 6c, 9b, and 10c are mainly mixed inhibitors on α-glucosidase and α-amylase. In addition, drug prediction and ADMET studies support that compounds 6c, 9b, and 10c are candidates with antidiabetic potential.
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Affiliation(s)
- Dolores G Aguila-Muñoz
- Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Carretera Estatal Santa Inés Tecuexcomax-Tepetitla, Km 1.5, Tepetitla de Lardizábal, Tlaxcala 90700, Mexico
| | - Gabriel Vázquez-Lira
- Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Carretera Estatal Santa Inés Tecuexcomax-Tepetitla, Km 1.5, Tepetitla de Lardizábal, Tlaxcala 90700, Mexico
| | - Erika Sarmiento-Tlale
- Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Carretera Estatal Santa Inés Tecuexcomax-Tepetitla, Km 1.5, Tepetitla de Lardizábal, Tlaxcala 90700, Mexico
| | - María C Cruz-López
- Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Carretera Estatal Santa Inés Tecuexcomax-Tepetitla, Km 1.5, Tepetitla de Lardizábal, Tlaxcala 90700, Mexico
| | - Fabiola E Jiménez-Montejo
- Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Carretera Estatal Santa Inés Tecuexcomax-Tepetitla, Km 1.5, Tepetitla de Lardizábal, Tlaxcala 90700, Mexico
| | - Víctor E López Y López
- Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Carretera Estatal Santa Inés Tecuexcomax-Tepetitla, Km 1.5, Tepetitla de Lardizábal, Tlaxcala 90700, Mexico
| | - Carlos H Escalante
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico
| | - Dulce Andrade-Pavón
- Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu S/N, Mexico City 11340, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico
| | - Omar Gómez-García
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico
| | - Joaquín Tamariz
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico
| | - Aarón Mendieta-Moctezuma
- Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Carretera Estatal Santa Inés Tecuexcomax-Tepetitla, Km 1.5, Tepetitla de Lardizábal, Tlaxcala 90700, Mexico
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13
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Maity P, Chatterjee J, Patil KT, Arora S, Katiyar MK, Kumar M, Samarbakhsh A, Joshi G, Bhutani P, Chugh M, Gavande NS, Kumar R. Targeting the Epidermal Growth Factor Receptor with Molecular Degraders: State-of-the-Art and Future Opportunities. J Med Chem 2023; 66:3135-3172. [PMID: 36812395 DOI: 10.1021/acs.jmedchem.2c01242] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Epidermal growth factor receptor (EGFR) is an oncogenic drug target and plays a critical role in several cellular functions including cancer cell growth, survival, proliferation, differentiation, and motility. Several small-molecule tyrosine kinase inhibitors (TKIs) and monoclonal antibodies (mAbs) have been approved for targeting intracellular and extracellular domains of EGFR, respectively. However, cancer heterogeneity, mutations in the catalytic domain of EGFR, and persistent drug resistance limited their use. Different novel modalities are gaining a position in the limelight of anti-EGFR therapeutics to overcome such limitations. The current perspective reflects upon newer modalities, importantly the molecular degraders such as PROTACs, LYTACs, AUTECs, and ATTECs, etc., beginning with a snapshot of traditional and existing anti-EGFR therapies including small molecule inhibitors, mAbs, and antibody drug conjugates (ADCs). Further, a special emphasis has been made on the design, synthesis, successful applications, state-of-the-art, and emerging future opportunities of each discussed modality.
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Affiliation(s)
- Pritam Maity
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
| | - Joydeep Chatterjee
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
| | - Kiran T Patil
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
| | - Sahil Arora
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
| | - Madhurendra K Katiyar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
| | - Manvendra Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
| | - Amirreza Samarbakhsh
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan 48201, United States
| | - Gaurav Joshi
- Department of Pharmaceutical Science, Hemvati Nandan Bahuguna Garhwal (A Central) University, Srinagar 246174, Dist. Garhwal (Uttarakhand), India
| | | | - Manoj Chugh
- In Vitro Diagnostics, Transasia BioMedical Pvt. Ltd. 400072 Mumbai, India
| | - Navnath S Gavande
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan 48201, United States.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48201, United States
| | - Raj Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, 151401 Bathinda, India
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14
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Threat of respiratory syncytial virus infection knocking the door: a proposed potential drug candidate through molecular dynamics simulations, a future alternative. J Mol Model 2023; 29:91. [PMID: 36884131 DOI: 10.1007/s00894-023-05489-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 02/24/2023] [Indexed: 03/09/2023]
Abstract
The discovery of antiviral approaches to prevent or cure respiratory syncytial virus (RSV) infections is critical, particularly because RSV is one of the most common causes of infant respiratory problems. There is currently no approved vaccination available to treat RSV infections. FDA has approved the drug ribavirin, but it is not sufficient to treat RSV. This work aimed to find and study in silico anti-RSV drugs that target matrix protein and nucleoprotein. In this study, we have identified five drug candidates that had better binding energies than ribavirin. Garenoxacin appeared as top lead compounds between them. AutoDock Vina was used to execute molecular docking of a library of chosen chemicals. The high-score compound was then confirmed using the Maestro 12.3 module's molecular dynamics simulation and the binding energies derived using Prime/Molecular Mechanics Generalized Born Surface Area (Prime/MM-GBSA). Comparative molecular dynamics simulations revealed that garenoxacin has better stability and high residue contacts with high binding affinity than ribavirin. This study showed garenoxacin could prevent RSV infection better than ribavirin. In pursuing a more effective RSV control drug, additional research into these chemicals in vitro and in vivo is essential.
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15
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Yin J, Wen H, Chen H. Toxicity evaluation of main zopiclone impurities based on quantitative structure-activity relationship models and in vitro tests. J Appl Toxicol 2023; 43:230-241. [PMID: 35945809 DOI: 10.1002/jat.4376] [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: 05/06/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 01/17/2023]
Abstract
Toxicity evaluation of main zopiclone impurities can provide a basis for safety assessment and quality standards of zopiclone. In this study, the impurity profile of zopiclone was analyzed using forced degradation and related substances of zopiclone tablets using high-performance liquid chromatography (HPLC). Furthermore, various quantitative structure-activity relationship (QSAR) models were used to compare the toxicity, especially genotoxicity of two main zopiclone degradation impurities, namely, impurity B and 2-amino-5-chloropyridine. The predictive genotoxicity results were verified using an in vitro bacterial reverse mutation (Ames) test. Meanwhile, using zebrafish embryos as an animal model, zopiclone and its main impurities were analyzed at different concentrations, and their effects on zebrafish development, including embryonic teratogenesis and lethality, were examined. The results showed that impurity B and 2-amino-5-chloropyridine were the main degradation impurities of zopiclone; the latter's content increased with increase in the solution storage time. QSAR prediction and in vitro test results confirmed that both impurity B and 2-amino-5-chloropyridine were non-mutagenic and classified in the fifth impurity category. According to ICH M7 guidelines, these could be controlled as general non-mutagenic impurities. The relative toxicity to zebrafish embryo development was the highest for 2-amino-5-chloropyridine, followed by impurity B and zopiclone, and the malformation rate and mortality of embryos were concentration dependent. In conclusion, an increase in the control limit of 2-amino-5-chloropyridine is recommended when the quality standards of zopiclone materials and preparations are revised to ensure safety and quality control. The specific limit value of this impurity should be determined through further evaluation and research.
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Affiliation(s)
- Jie Yin
- National Institutes for Food and Drug Control, Key Laboratory of Chemical Drug Quality Research and Evaluation, National Medical Products Administration, Beijing, China
| | - Hairuo Wen
- National Institutes for Food and Drug Control, National Center for Drug Safety Evaluation and Monitoring, Beijing Key Laboratory of Drug Non-clinical Safety Evaluation and Research, Beijing, China
| | - Hua Chen
- National Institutes for Food and Drug Control, Key Laboratory of Chemical Drug Quality Research and Evaluation, National Medical Products Administration, Beijing, China
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16
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Chauhan M, Dhar ZA, Gorki V, Sharma S, Koul A, Bala S, Kaur R, Kaur S, Sharma M, Dhingra N. Exploration of anticancer potential of Lantadenes from weed Lantana camara: Synthesis, in silico, in vitro and in vivo studies. PHYTOCHEMISTRY 2023; 206:113525. [PMID: 36442578 DOI: 10.1016/j.phytochem.2022.113525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 06/16/2023]
Abstract
Naturally occurring pentacyclic triterpenoids and their semisynthetic analogues have engrossed increasing attention for their anticancer potential and exhibiting promising role in discovery of new anticancer agents. Present study include the semi synthetic modifications of Lantadenes from the weed Lantana carama and their structures delineation by FT-IR, 1H-NMR, 13C-NMR & mass spectroscopy. All the compounds were scrutinized for in vitro cytotoxicity, ligand receptor interaction and in vivo anticancer studies. Most of the novel analogues displayed potent antiproliferative activity against A375 & A431 cancer cell lines and found superior to parent Lantadenes. In particular, 3β-(4-Methoxybenzoyloxy)-22β-senecioyloxy-olean-12-en-28-oic acid was found to be most suitable compound, with IC50 value of 3.027 μM aganist A375 cell line having least docking score (-69.40 kcal/mol). Promising anticancer potential of the lead was further indicated by significant reduction in tumor volume and burden in two stage carcinoma model. These findings suggests that the Lantadene derivatives may hold promising potential for the intervention of skin cancers.
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Affiliation(s)
- Monika Chauhan
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India; School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, 248007, India.
| | - Zahid Ahmad Dhar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - Varun Gorki
- Parasitology Laboratory, Department of Zoology, Panjab University, Chandigarh, 160014, India
| | - Sonia Sharma
- Department Cum National Centre for Human Genome Studies and Research, Punjab University, Chandigarh, 160014, India
| | - Ashwani Koul
- Department of Biophysics, Panjab University, Chandigarh, 160014, India
| | - Shashi Bala
- Department of Biophysics, Panjab University, Chandigarh, 160014, India
| | - Ramandeep Kaur
- Department Cum National Centre for Human Genome Studies and Research, Punjab University, Chandigarh, 160014, India
| | - Sukhbir Kaur
- Parasitology Laboratory, Department of Zoology, Panjab University, Chandigarh, 160014, India
| | - Manu Sharma
- National Forensic Science University, Delhi Campus, India
| | - Neelima Dhingra
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India.
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17
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Conformational Sampling Deciphers the Chameleonic Properties of a VHL-Based Degrader. Pharmaceutics 2023; 15:pharmaceutics15010272. [PMID: 36678900 PMCID: PMC9861353 DOI: 10.3390/pharmaceutics15010272] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Chameleonicity (the capacity of a molecule to adapt its conformations to the environment) may help to identify orally bioavailable drugs in the beyond-Rule-of-5 chemical space. Computational methods to predict the chameleonic behaviour of degraders have not yet been reported and the identification of molecular chameleons still relies on experimental evidence. Therefore, there is a need to tune predictions with experimental data. Here, we employ PROTAC-1 (a passively cell-permeable degrader), for which NMR and physicochemical data prove the chameleonic behaviour, to benchmark the capacity of two conformational sampling algorithms and selection schemes. To characterize the conformational ensembles in both polar and nonpolar environments, we compute three molecular properties proven to be essential for cell permeability: conformer shape (radius of gyration), polarity (3D PSA), and the number of intramolecular hydrogen bonds. Energetic criteria were also considered. Infographics monitored the simultaneous variation of those properties in computed and NMR conformers. Overall, we provide key points for tuning conformational sampling tools to reproduce PROTAC-1 chameleonicity according to NMR evidence. This study is expected to improve the design of PROTAC drugs and the development of computational sustainable strategies to exploit the potential of new modalities in drug discovery.
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18
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Defining a generic column set for achiral supercritical fluid chromatography applied to pharmaceuticals or natural products. J Chromatogr A 2023; 1687:463667. [PMID: 36463646 DOI: 10.1016/j.chroma.2022.463667] [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: 10/05/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
When starting a method development in supercritical fluid chromatography (SFC), the first step is usually to screen several stationary phases based on previous experience or simply based on what is available in the laboratory. However, as there are now a large number of stationary phases available for SFC, the choice of an adequate set of columns to rapidly achieve a satisfying result can be difficult. In this project, 16 columns comprising a wide diversity of stationary phases and polarities ranging from the most polar (like bare silica gel) to the least polar (like octadecylbonded-silica) were compared, based on the gradient analysis of 129 probe compounds. The set mostly comprised active pharmaceutical ingredients, natural products and a few metabolites. The columns were ranked with the help of Derringer desirability functions taking account of (i) the number of compounds eluted from the column, (ii) the elution time in a suitable time frame, (iii) the average peak width, (iv) the average peak symmetry and (v) the spreading of retention along the gradient time. The five criteria selected showed no correlation. Overall, it appeared that those columns that had a high overall score were good for several reasons, like bare silica gel, propanediol-bonded silica or pentabromobenzyloxy-bonded silica. Initially, the columns had been screened with a gradient elution starting from 5% co-solvent and ending with 50% co-solvent in CO2. However, for some most retentive columns like amide-bonded silica, too many compounds remained non-eluted from the column. To examine this column more fairly, a second elution gradient was applied that ended with 100% co-solvent. This proved effective in restoring good overall performance through the elution of the most polar compounds.
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19
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Mitra D, Paul M, Thatoi H, Mohapatra PKD. Study of potentiality of dexamethasone and its derivatives against Covid-19. J Biomol Struct Dyn 2022; 40:10239-10249. [PMID: 34182880 DOI: 10.1080/07391102.2021.1942210] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In December 2019, COVID-19 epidemic was reported in Wuhan, China, and subsequently the infection has spread all over the world and became pandemic. The death toll associated with the pandemic is increasing day by day in a high rate. Herein, an effort has been made to identify the potentiality of commercially available drugs and also their probable derivatives for creation of better opportunity to make more powerful drugs against coronavirus. This study involves the in-silico interactions of dexamethasone and its derivatives against the multiple proteins of SARS-CoV-2 with the help of various computational methods. Descriptor parameters revealed their non-toxic effect in the human body. Ultimately docking studies and molecular dynamic simulation on those target protein by dexamethasone and its derivatives showed a high binding energy. Dexamethasone showed -9.8 kcal/mol and its derivative D5 showed -12.1 kcal/mol binding energy. Those scores indicate that dexamethasone has more therapeutic effect on SARS CoV-2 than other currently used drugs. Derivatives give the clue for the synthesis of a novel drug to remove SARS CoV-2. Until then, dexamethasone will be used as a potential inhibitor of SARS CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, West Bengal, India
| | - Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, Odisha, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, Odisha, India
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20
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Rossi Sebastiano M, Garcia Jimenez D, Vallaro M, Caron G, Ermondi G. Refinement of Computational Access to Molecular Physicochemical Properties: From Ro5 to bRo5. J Med Chem 2022; 65:12068-12083. [PMID: 36094896 PMCID: PMC9511483 DOI: 10.1021/acs.jmedchem.2c00774] [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] [Indexed: 11/29/2022]
Abstract
![]()
There is a need of computational tools to rank bRo5 drug
candidates
in the very early phases of drug discovery when chemical matter is
unavailable. In this study, we selected three compounds: (a) a Ro5
drug (Pomalidomide), (b) a bRo5 orally available drug (Saquinavir),
and (c) a polar PROTAC (CMP 98) to focus on computational access to
physicochemical properties. To provide a benchmark, the three compounds
were first experimentally characterized for their lipophilicity, polarity,
IMHBs, and chameleonicity. To reproduce the experimental information
content, we generated conformer ensembles with conformational sampling
and molecular dynamics in both water and nonpolar solvents. Then we
calculated Rgyr, 3D PSA, and IMHB number. An innovative pool of strategies
for data analysis was then provided. Overall, we report a contribution
to close the gap between experimental and computational methods for
characterizing bRo5 physicochemical properties.
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Affiliation(s)
- Matteo Rossi Sebastiano
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Diego Garcia Jimenez
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
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21
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In silico drug design and molecular docking of novel amidophosphonates and sulfamidophosphonates as inhibitors of urokinase-type plasminogen activator. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Novel psoralen derivatives as anti-breast cancer agents and their light-activated cytotoxicity against HER2 positive breast cancer cells. Sci Rep 2022; 12:13487. [PMID: 35931753 PMCID: PMC9356065 DOI: 10.1038/s41598-022-17625-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/28/2022] [Indexed: 11/25/2022] Open
Abstract
Psoralen derivatives are well known for their unique phototoxicity and also exhibits promising anti-breast cancer activity both in the presence and the absence of UVA irradiation. However, the structure–activity relationship on this scaffold remains lacking. Herein, a series of psoralen derivatives with various C-5 substituents were synthesized and evaluated for their in vitro dark and light-activated cytotoxicity against three breast cancer cell lines: MDA-MB-231, T47-D, and SK-BR-3. The type of substituents dramatically impacted the activity, with the 4-bromobenzyl amide derivative (3c) exhibiting the highest dark cytotoxicity against T47-D (IC50 = 10.14 µM), with the activity comparable to those of the reference drugs (doxorubicin, 1.46 µM; tamoxifen citrate, 20.86 µM; lapatinib 9.78 µM). On the other hand, the furanylamide 3g exhibits the highest phototoxicity against SK-BR-3 cells with the IC50 of 2.71 µM, which is almost tenfold increase compared to the parent compound, methoxsalen. Moreover, these derivatives showed exceptional selectivity towards HER2+ (SK-BR-3) over the HER2− (MDA-MB-231) breast cancer cell lines, which correlates well with the results from the molecular docking study, revealing that 3g formed favorable interactions within the active site of the HER2. Additionally, the cell morphology of SK-BR-3 cells suggested that the significant phototoxicity was related to induction of cell apoptosis. Most of the synthesized psoralen derivatives possess acceptable physicochemical properties and are suitable for being further developed as a novel anti-breast cancer agent in the future.
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QSAR, Docking, and Molecular Dynamics Simulation Studies of Sigmacidins as Antimicrobials against Streptococci. Int J Mol Sci 2022; 23:ijms23084085. [PMID: 35456906 PMCID: PMC9025105 DOI: 10.3390/ijms23084085] [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: 03/10/2022] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 12/02/2022] Open
Abstract
Streptococci are a family of bacterial species significantly affecting human health. In addition, environmental Streptococci represent one of the major causes of diverse livestock diseases. Due to antimicrobial resistance, there is an urgent need for novel antimicrobial agent discovery against Streptococci. We discovered a class of benzoic acid derivatives named sigmacidins inhibiting the bacterial RNA polymerase-σ factor interaction and demonstrating excellent antimicrobial activity against Streptococci. In this work, a combinational computer approach was applied to gain insight into the structural basis and mechanism of action of sigmacidins as antimicrobials against Streptococcus pneumoniae. Both two- and three-dimensional quantitative structure-active relationships (2D and 3D QSAR) of sigmacidins displayed good predictive ability. Moreover, molecular docking and molecular dynamics simulation studies disclosed possible contacts between the inhibitors and the protein. The results obtained in this study provided understanding and new directions to the further optimizations of sigmacidins as novel antimicrobials.
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Ramesh D, Sarkar D, Joji A, Singh M, Mohanty AK, G Vijayakumar B, Chatterjee M, Sriram D, Muthuvel SK, Kannan T. First-in-class pyrido[2,3-d]pyrimidine-2,4(1H,3H)-diones against leishmaniasis and tuberculosis: Rationale, in vitro, ex vivo studies and mechanistic insights. Arch Pharm (Weinheim) 2022; 355:e2100440. [PMID: 35106845 DOI: 10.1002/ardp.202100440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/22/2021] [Accepted: 01/07/2022] [Indexed: 11/06/2022]
Abstract
Pyrido[2,3-d]pyrimidine-2,4(1H,3H)-diones were synthesized, for the first time, from indole chalcones and 6-aminouracil, and their ability to inhibit leishmaniasis and tuberculosis (Tb) infections was evaluated. The in vitro antileishmanial activity against promastigotes of Leishmania donovani revealed exceptional activities of compounds 3, 12 and 13, with IC50 values ranging from 10.23 ± 1.50 to 15.58 ± 1.67 µg/ml, which is better than the IC50 value of the standard drug pentostam of 500 μg/ml. The selectivity of the compounds towards Leishmania parasites was evaluated via ex vivo studies in Swiss albino mice. The efficiency of these compounds against Tb infection was then evaluated using the in vitro anti-Tb microplate Alamar Blue assay. Five compounds, 3, 7, 8, 9 and 12, showed MIC100 values against the Mycobacterium tuberculosis H37 Rv strain at 25 µg/ml, and compound 20 yielded an MIC100 value of 50 µg/ml. Molecular modelling of these compounds highlighted interactions with binding sites of dihydrofolate reductase, pteridine reductase and thymidylate kinase, thus establishing the rationale of their pharmacological activity against both pathogens, which is consistent with the in vitro results. From the above results, it is clear that compounds 3 and 12 are promising lead candidates for Leishmania and Mycobacterium infections and may be promising for coinfections.
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Affiliation(s)
- Deepthi Ramesh
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry, India
| | - Deblina Sarkar
- Department of Pharmacology, Institute of Post Graduate Medical Education & Research (IPGME&R), Kolkata, West Bengal, India
| | - Annu Joji
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry, India
| | - Monica Singh
- Department of Pharmacy, Birla Institute of Technology & Science Pilani, Hyderabad, India
| | - Amaresh K Mohanty
- Department of Bioinformatics, Pondicherry University, Kalapet, Puducherry, India
| | | | - Mitali Chatterjee
- Department of Pharmacology, Institute of Post Graduate Medical Education & Research (IPGME&R), Kolkata, West Bengal, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology & Science Pilani, Hyderabad, India
| | - Suresh K Muthuvel
- Department of Bioinformatics, Pondicherry University, Kalapet, Puducherry, India
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Waziri I, Isa MA, Sonopo M, Williams DBG, Muller A. Synthesis, anti-microbial, toxicity and molecular docking studies of N-nitroso-N-phenylhydroxylamine (cupferron) and its derivatives. Bioorg Med Chem Lett 2021; 52:128381. [PMID: 34571137 DOI: 10.1016/j.bmcl.2021.128381] [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: 05/10/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 10/20/2022]
Abstract
Bacterial resistance to antimicrobial agents is increasing at an alarming rate globally and requires new lead compounds for antibiotics. In this study, N-phenyl-N-nitroso hydroxylamine (cupferron) and its derivatives have been synthesised using readily available starting materials. The compounds were obtained in high yield and purity. They show activity towards a range of Gram-positive and Gram-negative pathogenic bacteria, with minimum inhibitory concentration (MIC) values as low as 2 μg.mL-1 against the tested organisms, especially for Gram-positive species. Toxicity studies on the lead compound 3b indicate insignificant effects on healthy cell lines. Molecular docking studies on the lead compound identify possible binding modes of the compound, and the results obtained correlate with those of in vitro and MIC studies. The lead compound shows excellent drug-likeness properties.
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Affiliation(s)
- Ibrahim Waziri
- Department of Chemical Sciences, University of Johannesburg, P.O. Box 524, Auckland Park 2006, South Africa
| | - Mustafa A Isa
- Department of Microbiology, University of Maiduguri, P.M.B. 1069, Maiduguri, Nigeria
| | - Molahlehi Sonopo
- Radiochemistry, Department of Applied Chemistry, Necsa (South African Nuclear Energy Corporation Ltd.), P.O. Box 582, Pretoria 0001, South Africa
| | - D Bradley G Williams
- University of Technology Sydney, School of Mathematical and Physical Sciences, P.O. Box 123, Broadway, Sydney, NSW 2007, Australia.
| | - Alfred Muller
- Department of Chemical Sciences, University of Johannesburg, P.O. Box 524, Auckland Park 2006, South Africa.
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Rowaiye AB, Mendes YJT, Olofinsae SA, Oche JB, Oladipo OH, Okpalefe OA, Ogidigo JO. Camptothecin shows better promise than Curcumin in the inhibition of the Human Telomerase: A computational study. Heliyon 2021; 7:e07742. [PMID: 34485722 PMCID: PMC8405929 DOI: 10.1016/j.heliyon.2021.e07742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/17/2021] [Accepted: 08/05/2021] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES The Human Telomerase enzyme has become a drug target in the treatment of cancers and age-related disorders. This study aims to identify potential natural inhibitors of the Human Telomerase from compounds derived from edible African plants. MATERIALS AND METHODS A library of 1,126 natural compounds was molecularly docked against the Telomerase Reverse Transcriptase (PDB ID: 5ugw), the catalytic subunit of the target protein. Curcumin, a known Telomerase inhibitor was used as the standard. The front-runner compounds were screened for bioavailability, pharmacokinetic properties, and bioactivity using the SWISSADME, PKCSM, and Molinspiration webservers respectively. The molecular dynamic simulation and analyses of the apo and holo proteins were performed by the Galaxy supercomputing webserver. RESULTS The results of the molecular docking and virtual screening reveal Augustamine and Camptothecin as lead compounds. Augustamine has better drug-likeness and pharmacokinetic properties while Camptothecin showed better bioactivity and stronger binding affinity (-8.2 kcal/mol) with the target. The holo structure formed by Camptothecin showed greater inhibitory activity against the target with a total RMSF of 169.853, B-Factor of 20.164, and 108 anti-correlating residues. CONCLUSION Though they both act at the same binding site, Camptothecin induces greater Telomerase inhibition and better molecular stability than the standard, Curcumin. Further tests are required to investigate the inhibitory activities of the lead compounds.
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Affiliation(s)
| | | | - Samson Ayodeji Olofinsae
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | | | | | | | - Joyce Oloaigbe Ogidigo
- Bioresources Development Centre, National Biotechnology Development Agency, Abuja, Nigeria
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Begnini F, Poongavanam V, Atilaw Y, Erdelyi M, Schiesser S, Kihlberg J. Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies. ACS Med Chem Lett 2021; 12:983-990. [PMID: 34136079 PMCID: PMC8201747 DOI: 10.1021/acsmedchemlett.1c00126] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022] Open
Abstract
![]()
Conformation-dependent 3D descriptors
have been shown to provide
better predictions of the physicochemical properties of macrocycles
than 2D descriptors. However, the computational identification of
relevant conformations for macrocycles is nontrivial. Herein, we report
that the Caco-2 cell permeability difference between a pair of diastereomeric
macrocycles correlated with their solvent accessible 3D polar surface
area and radius of gyration. The descriptors were calculated from
the macrocycles’ solution-phase conformational ensembles and
independently from ensembles obtained by conformational sampling.
Calculation of the two descriptors for three other stereo- and regioisomeric
macrocycles also allowed the correct ranking of their cell permeability.
Methods for conformational sampling may thus allow ranking of passive
permeability for moderately flexible macrocycles, thereby contributing
to the prioritization of macrocycles for synthesis in lead optimization.
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Affiliation(s)
- Fabio Begnini
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | | | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Stefan Schiesser
- Department of Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
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Zhang S, Liu C, Yang D, Ruan J, Luo Z, Quan P, Fang L. Mechanism insight on drug skin delivery from polyurethane hydrogels: Roles of molecular mobility and intermolecular interaction. Eur J Pharm Sci 2021; 161:105783. [PMID: 33667662 DOI: 10.1016/j.ejps.2021.105783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/01/2021] [Accepted: 02/25/2021] [Indexed: 10/22/2022]
Abstract
Though polyurethane (PU) hydrogel had great potential in topical drug delivery system, drug skin delivery behavior from hydrogel and the underlying molecular mechanism were still unclear. In this study, PU and Carbomer (CP as control) hydrogels were prepared with lidocaine (LID) and ofloxacin (OFX) as model drugs. In vitro skin permeation and tissue distribution study were conducted to evaluate the drug delivery behaviors. The underlying molecular mechanisms were characterized by drug release with octanol as release medium, rheological study, ATR-FTIR, NMR, and molecular simulation. The results showed that the skin permeation amount of LID-PU (45.50 ± 7.12 μg) was lower than LID-CP (45.50 ± 7.12 μg). And the LID diffusion coefficient of PU (26.21 μg/h0.5) was also lower than CP (31.30 μg/h0.5), which attributed to H-bonding between LID (-CONH) and PU (-NHCOO). However, the OFX-PU showed a higher skin permeation amount (10.06 ± 1.29 μg) than OFX-CP (5.28 ± 1.39 μg). And the OFX-PU also showed a higher diffusion coefficient (30.0 μg/h0.5) than OFX-CP (21.37 μg/h0.5), which was caused by increased mobility of hydrogel when interaction action site was C-O-C in PU. In conclusion, drug skin delivery behavior from PU hydrogel was controlled by molecular mobility and intermolecular interaction, which clarified the influence of the functional group of PU hydrogel on drug skin delivery behavior and broadened our understanding of PU hydrogel application in topical drug delivery system.
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Affiliation(s)
- Shuai Zhang
- Department of Pharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning, 110016, China
| | - Chao Liu
- Department of Pharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning, 110016, China
| | - Degong Yang
- Department of Pharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning, 110016, China
| | - Jiuheng Ruan
- Department of Pharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning, 110016, China
| | - Zheng Luo
- Department of Pharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning, 110016, China
| | - Peng Quan
- Department of Pharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning, 110016, China
| | - Liang Fang
- Department of Pharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning, 110016, China.
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29
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Joshi G, Sindhu J, Thakur S, Rana A, Sharma G, Mayank, Poduri R. Recent efforts for drug identification from phytochemicals against SARS-CoV-2: Exploration of the chemical space to identify druggable leads. Food Chem Toxicol 2021; 152:112160. [PMID: 33823228 PMCID: PMC8018909 DOI: 10.1016/j.fct.2021.112160] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023]
Abstract
Nature, which remains a central drug discovery pool, is always looked upon to find a putative druggable lead. The natural products and phytochemical derived from plants are essential during a global health crisis. This class represents one of the most practical and promising approaches to decrease pandemic's intensity owing to their therapeutic potential. The present manuscript is therefore kept forth to give the researchers updated information on undergoing research in allied areas of natural product-based drug discovery, particularly for Covid-19 disease. The study briefly shreds evidence from in vitro and in silico researches done so far to find a lead molecule against Covid-19. Following this, we exhaustively explored the concept of chemical space and molecular similarity parameters for the drug discovery about the lead(s) generated from in silico-based studies. The comparison was drawn using FDA-approved anti-infective agents during 2015–2020 using key descriptors to evaluate druglike properties. The outcomes of results were further corroborated using Molecular Dynamics studies which suggested the outcomes in alignment with chemical space ranking. In a nutshell, current research work aims to provide a holistic strategic approach to drug design, keeping in view the identified phytochemicals against Covid-19.
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Affiliation(s)
- Gaurav Joshi
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Bathinda, 151 401, India; School of Pharmacy, Graphic Era Hill University, Dehradun, 248171, India.
| | - Jayant Sindhu
- Department of Chemistry, COBS & H, CCS Haryana Agricultural University, Hisar, 125 004 India
| | - Shikha Thakur
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Bathinda, 151 401, India
| | - Abhilash Rana
- Amity Institute of Biotechnology, Amity University, Sector 125 Noida, Uttar Pradesh, India
| | - Geetika Sharma
- Amity Institute of Biotechnology, Amity University, Sector 125 Noida, Uttar Pradesh, India
| | - Mayank
- Shobhaben Pratapbhai Patel - School of Pharmacy & Technology Management, SVKM's NMIMS University, Vile Parle, Mumbai, 400056, India.
| | - Ramarao Poduri
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Bathinda, 151 401, India.
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30
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Yang D, Liu C, Ding D, Quan P, Fang L. The molecular design of drug-ionic liquids for transdermal drug delivery: Mechanistic study of counterions structure on complex formation and skin permeation. Int J Pharm 2021; 602:120560. [PMID: 33798684 DOI: 10.1016/j.ijpharm.2021.120560] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/24/2021] [Accepted: 03/27/2021] [Indexed: 12/22/2022]
Abstract
Though ionic liquids (ILs) as novel enhancers had garnered wide attention, detailed studies elucidating molecular design of drug-ILs were missing and mechanisms of their formation and skin permeation were still lacking. Herein, we systematically investigated effects of counterions structures on formation and skin permeation of drug-ILs. Firstly, effects of counterions on formation of drug-ILs were dependent on polarizability, molecular weight (M.W.) and polar surface area of counterions. It was caused by strong charge assisted hydrogen bond and van der Waals interactions revealed through FT-IR, X-ray photoelectron spectroscopy and molecular docking, which undermined ionic interactions and reduced total interaction strength, thereby produced lower lattice energy. Then, skin permeability of drug-ILs had a good parabola relationship with M.W., polarizability and log P of counterions. The underlying mechanism was the increased drug miscibility with stratum corneum, which caused conformational disorder and phase transition of lipid bilayers characterized by ATR-FTIR, DSC and confocal laser scanning microscopy. Finally, the drug-ILs proved to be non-irritating using in vivo skin erythema analysis. In conclusion, the quantitative structure-activity relationship models based on counterions structure to predict formation and skin permeation of drug-ILs were developed, which provided basic theory for design of drug-ILs with high permeation-enhancing efficiency.
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Affiliation(s)
- Degong Yang
- Department of Pharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, China
| | - Chao Liu
- Department of Pharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, China.
| | - Dawei Ding
- Department of Pharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, China
| | - Peng Quan
- Department of Pharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, China
| | - Liang Fang
- Department of Pharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, China.
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31
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Bhutani P, Joshi G, Raja N, Bachhav N, Rajanna PK, Bhutani H, Paul AT, Kumar R. U.S. FDA Approved Drugs from 2015-June 2020: A Perspective. J Med Chem 2021; 64:2339-2381. [PMID: 33617716 DOI: 10.1021/acs.jmedchem.0c01786] [Citation(s) in RCA: 241] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In the present work, we report compilation and analysis of 245 drugs, including small and macromolecules approved by the U.S. FDA from 2015 until June 2020. Nearly 29% of the drugs were approved for the treatment of various types of cancers. Other major therapeutic areas of focus were infectious diseases (14%); neurological conditions (12%); and genetic, metabolic, and cardiovascular disorders (7-8% each). Itemization of the approved drugs according to the year of approval, sponsor, target, chemical class, major drug-metabolizing enzyme(s), route of administration/elimination, and drug-drug interaction liability (perpetrator or/and victim) is presented and discussed. An effort has been made to analyze the pharmacophores to identify the structural (e.g., aromatic, heterocycle, and aliphatic), elemental (e.g., boron, sulfur, fluorine, phosphorus, and deuterium), and functional group (e.g., nitro drugs) diversity among the approved drugs. Further, descriptor-based chemical space analysis of FDA approved drugs and several strategies utilized for optimizing metabolism leading to their discoveries have been emphasized. Finally, an analysis of drug-likeness for the approved drugs is presented.
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Affiliation(s)
- Priyadeep Bhutani
- Pharmaceutical Candidate Optimization, Biocon Bristol-Myers Squibb R&D Centre, Syngene International Limited, Bangalore 560099, India.,Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan 333031, India
| | - Gaurav Joshi
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151001, India
| | - Nivethitha Raja
- Pharmaceutical Candidate Optimization, Biocon Bristol-Myers Squibb R&D Centre, Syngene International Limited, Bangalore 560099, India
| | - Namrata Bachhav
- 1015 E Cozza Drive # 12, Spokane Washington 99208, United States
| | - Prabhakar K Rajanna
- Pharmaceutical Candidate Optimization, Biocon Bristol-Myers Squibb R&D Centre, Syngene International Limited, Bangalore 560099, India
| | - Hemant Bhutani
- Pharmaceutical Development, Biocon Bristol-Myers Squibb R&D Centre, Bristol-Myers Squibb India Private Limited, Bangalore 560099, India
| | - Atish T Paul
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan 333031, India
| | - Raj Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151001, India
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Tyszka-Czochara M, Adach A, Grabowski T, Konieczny P, Pasko P, Ortyl J, Świergosz T, Majka M. Selective Cytotoxicity of Complexes with N,N,N-Donor Dipodal Ligand in Tumor Cells. Int J Mol Sci 2021; 22:ijms22041802. [PMID: 33670389 PMCID: PMC7917659 DOI: 10.3390/ijms22041802] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/27/2021] [Accepted: 02/08/2021] [Indexed: 11/16/2022] Open
Abstract
The present article demonstrates selective cytotoxicity against cancer cells of the complexes [Co(LD)2]I2∙CH3OH (1), [CoLD(NCS)2] (2) and [VOLD(NCS)2]∙C6H5CH3 (3) containing the dipodal tridentate ligand LD = N,N-bis(3,5-dimethylpyrazol-1-ylmethyl)amine), formed in situ. All tested complexes expressed greater anticancer activities and were less toxic towards noncancerous cells than cisplatin. Cobalt complexes (1 and 2) combined high cytotoxicity with selectivity towards cancer cells and caused massive tumour cell death. The vanadium complex (3) induced apoptosis specifically in cancer cells and targeted proteins, controlling their invasive and metastatic properties. The presented experimental data and computational prediction of drug ability of coordination compounds may be helpful for designing novel and less toxic metal-based anticancer species with high specificities towards tumour cells.
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Affiliation(s)
| | - Anna Adach
- Institute of Chemistry, Jan Kochanowski University, 25-406 Kielce, Poland;
| | | | - Paweł Konieczny
- Faculty of Medicine, Jagiellonian University Medical College, 30-663 Krakow, Poland; (P.K.); (M.M.)
| | - Paweł Pasko
- Faculty of Pharmacy, Jagiellonian University Medical College, 30-688 Krakow, Poland;
| | - Joanna Ortyl
- Department of Biotechnology and Physical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, 31-155 Kraków, Poland;
- Photo HiTech Ltd., Life Science Park, Bobrzyńskiego 14, 30-348 Cracow, Poland
| | - Tomasz Świergosz
- Department of Analytical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, 31-155 Kraków, Poland;
| | - Marcin Majka
- Faculty of Medicine, Jagiellonian University Medical College, 30-663 Krakow, Poland; (P.K.); (M.M.)
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Nkambeu B, Ben Salem J, Beaudry F. Eugenol and Other Vanilloids Hamper Caenorhabditis elegans Response to Noxious Heat. Neurochem Res 2020; 46:252-264. [PMID: 33123873 DOI: 10.1007/s11064-020-03159-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 10/23/2022]
Abstract
Eugenol, a known vanilloid, was frequently used in dentistry as a local analgesic in addition, antibacterial and neuroprotective effects were also reported. Eugenol, capsaicin and many vanilloids are interacting with the transient receptor potential vanilloid 1 (TRPV1) in mammals and the TRPV1 is activated by noxious heat. The pharmacological manipulation of the TRPV1 has been shown to have therapeutic value. Caenorhabditis elegans (C. elegans) express TRPV orthologs (e.g. OCR-2, OSM-9) and it is a commonly used animal model system to study nociception as it displays a well-defined and reproducible nocifensive behavior. After exposure to vanilloid solutions, C. elegans wild type (N2) and mutants were placed on petri dishes divided in quadrants for heat stimulation. Thermal avoidance index was used to phenotype each tested C. elegans experimental groups. The results showed that eugenol, vanillin and zingerone can hamper nocifensive response of C. elegans to noxious heat (32-35 °C) following a sustained exposition. Also, the effect was reversed 6 h post exposition. Furthermore, eugenol and vanillin did not target specifically the OCR-2 or OSM-9 but zingerone did specifically target the OCR-2 similarly to capsaicin. Further structural and physicochemical analyses were performed. Key parameters for quantitative structure-property relationships (QSPR), quantitative structure-activity relationships (QSAR) and frontier orbital analyses suggest similarities and dissimilarities amongst the tested vanilloids and capsaicin in accordance with the relative anti-nociceptive effects observed.
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Affiliation(s)
- Bruno Nkambeu
- Groupe de Recherche en Pharmacologie Animal du Québec (GREPAQ), Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, Saint-Hyacinthe, QC, J2S 2M2, Canada.,Centre de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montréal, QC, Canada
| | - Jennifer Ben Salem
- Groupe de Recherche en Pharmacologie Animal du Québec (GREPAQ), Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, Saint-Hyacinthe, QC, J2S 2M2, Canada.,Centre de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montréal, QC, Canada.,Institut des Maladies Métaboliques et Cardiovasculaires, INSERM UMR1048, Université de Toulouse, Toulouse, France
| | - Francis Beaudry
- Groupe de Recherche en Pharmacologie Animal du Québec (GREPAQ), Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, Saint-Hyacinthe, QC, J2S 2M2, Canada. .,Centre de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montréal, QC, Canada.
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34
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Pathak P, Naumovich V, Grishina M, Potemkin V. The study of EGFR-ligand complex electron property relationship with biological activity. J Biomol Struct Dyn 2020; 40:375-388. [PMID: 32897174 DOI: 10.1080/07391102.2020.1813629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The present investigation grounded on estimation of electron properties of the structures of EGFR proteins-ligand complexes using our laboratory-developed methodology AlteQ approach, which describes the molecular electron density of the complex in space for a certain point in three-dimensional coordinates. Briefly, the system embodies molecular electron density as a sum of Slater's type atomic increments of the molecular system. Further, using this methodology, we calculated different electron characteristics of selected EGFR protein-ligand complexes and established the relationship between different electron properties with their experimental pharmacological activity value (pIC50). The study suggested that EGFR inhibitory activity has higher correlation with intermolecular contacts of H with pi-system of aromatic ring between protein and ligands. Therefore, this created model has impact to identify and design potential ligands against EGFR in anticancer drug discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prateek Pathak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladislav Naumovich
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
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35
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Yang D, Liu C, Quan P, Fang L. A systematic approach to determination of permeation enhancer action efficacy and sites: Molecular mechanism investigated by quantitative structure−activity relationship. J Control Release 2020; 322:1-12. [DOI: 10.1016/j.jconrel.2020.03.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/23/2020] [Accepted: 03/10/2020] [Indexed: 02/06/2023]
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36
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Russo G, Barbato F, Grumetto L, Philippe L, Lynen F, Goetz GH. Entry of therapeutics into the brain: Influence of exposed polarity calculated in silico and measured in vitro by supercritical fluid chromatography. Int J Pharm 2019; 560:294-305. [DOI: 10.1016/j.ijpharm.2019.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 01/18/2019] [Accepted: 02/08/2019] [Indexed: 12/23/2022]
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37
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Poongavanam V, Danelius E, Peintner S, Alcaraz L, Caron G, Cummings MD, Wlodek S, Erdelyi M, Hawkins PCD, Ermondi G, Kihlberg J. Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations? ACS OMEGA 2018; 3:11742-11757. [PMID: 30320271 PMCID: PMC6173504 DOI: 10.1021/acsomega.8b01379] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/04/2018] [Indexed: 05/03/2023]
Abstract
Conformational flexibility is a major determinant of the properties of macrocycles and other drugs in beyond rule of 5 (bRo5) space. Prediction of conformations is essential for design of drugs in this space, and we have evaluated three tools for conformational sampling of a set of 10 bRo5 drugs and clinical candidates in polar and apolar environments. The distance-geometry based OMEGA was found to yield ensembles spanning larger structure and property spaces than the ensembles obtained by MOE-LowModeMD (MOE) and MacroModel (MC). Both MC and OMEGA but not MOE generated different ensembles for polar and apolar environments. All three conformational search methods generated conformers similar to the crystal structure conformers for 9 of the 10 compounds, with OMEGA performing somewhat better than MOE and MC. MOE and OMEGA found all six conformers of roxithromycin that were identified by NMR in aqueous solutions, whereas only OMEGA sampled the three conformers observed in chloroform. We suggest that characterization of conformers using molecular descriptors, e.g., the radius of gyration and polar surface area, is preferred to energy- or root-mean-square deviation-based methods for selection of biologically relevant conformers in drug discovery in bRo5 space.
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Affiliation(s)
| | - Emma Danelius
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen
10, SE-41296 Gothenburg, Sweden
| | - Stefan Peintner
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - Lilian Alcaraz
- Medicinal
Chemistry, Johnson & Johnson Innovation, One Chapel Place, London W1G 0BG, U.K.
| | - Giulia Caron
- Department
of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135 Torino, Italy
| | - Maxwell D. Cummings
- Janssen
Research & Development, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Stanislaw Wlodek
- OpenEye
Scientific Software, 9 Bisbee Court, Santa Fe, New Mexico 87508, United States
| | - Mate Erdelyi
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
- The
Swedish NMR Centre, Medicinaregatan
5, SE-405 30 Gothenburg, Sweden
| | - Paul C. D. Hawkins
- OpenEye
Scientific Software, 9 Bisbee Court, Santa Fe, New Mexico 87508, United States
| | - Giuseppe Ermondi
- Department
of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135 Torino, Italy
- E-mail: . Phone: +39 (0)11 6708337 (G.E.)
| | - Jan Kihlberg
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
- E-mail: . Phone: +46 (0)18 4713801 (J.K.)
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38
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Qian J, Han Y, Li J, Zhang J, Hu C. Toxic effect prediction of cefatirizine amidine sodium and its impurities by structure-toxicity relationship of cephalosporins. Toxicol In Vitro 2017; 46:137-147. [PMID: 28963076 DOI: 10.1016/j.tiv.2017.09.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 08/26/2017] [Accepted: 09/21/2017] [Indexed: 11/30/2022]
Abstract
The three-dimensional (3D) structure-toxicity relationship of cephalosporins was explored by computing the most stable conformations of 33 kinds of cephalosporins in aqueous solution and using the teratogenicity and lethality of these compounds obtained in zebrafish embryo toxicity testing to evaluate their toxic effects. The toxic effect of cefatirizine amidine sodium, a novel cephalosporin which has finished preclinical study, was investigated. It is thought that the teratogenic effect of the triazine ring at the C-3 position is the main toxic effect of cefatirizine amidine. In addition, cefatirizine amidine is no more toxic than cefathiamidine and ceftriaxone. The results of the zebrafish embryo toxicity test combined with gene expression microarray technology were consistent with the prediction. The toxic effects of some potential process-related impurities of cefatirizine amidine were also predicted.
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Affiliation(s)
- Jianqin Qian
- National Institutes for Food and Drug Control, 100050 Beijing, China; ZheJiang Institute for Food and Drug Control, 310000 Hangzhou, Zhejiang, China
| | - Ying Han
- National Institutes for Food and Drug Control, 100050 Beijing, China; Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, 100050 Beijing, China
| | - Jin Li
- National Institutes for Food and Drug Control, 100050 Beijing, China
| | - Jingpu Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, 100050 Beijing, China.
| | - Changqin Hu
- National Institutes for Food and Drug Control, 100050 Beijing, China.
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39
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Molecular descriptors for polarity: the need for going beyond polar surface area. Future Med Chem 2016; 8:2013-2016. [DOI: 10.4155/fmc-2016-0165] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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40
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Wu D, Lucy CA. Study of the slope of the linear relationship between retention and mobile phase composition (Snyder-Soczewiñski model) in normal phase liquid chromatography with bonded and charge-transfer phases. J Chromatogr A 2016; 1475:31-40. [PMID: 27852455 DOI: 10.1016/j.chroma.2016.10.068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/23/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022]
Abstract
The Snyder model and the Soczewiñski model are compared on classic NPLC bonded phases using literature data, and on the charge transfer 2, 4-dinitroanilinopropyl (DNAP) column using experimentally collected data. Overall, the Snyder model slightly better predicts the n-slope than the Soczewiñski model. However, both models give comparable uncertainty in predicting n-slope for a given compound. The number of aromatic double bonds was the most suitable descriptor for estimating the relative n-slope of PAHs, as it correlated with behavior better than the number of aromatic rings and is simpler to calculate than the solute adsorption area. On the DNAP phase, a modified Soczewiñski model is suggested to allow for the significant contribution of the aromatic rings to the n-slope. For classic NPLC bonded phases and DNAP columns, the contribution of polar group to the n-slope parallels the adsorption energy of each polar group.
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Affiliation(s)
- Di Wu
- Department of Chemistry, University of Alberta, Gunning/Lemieux Chemistry Centre, Edmonton, Alberta T6G 2G2 Canada
| | - Charles A Lucy
- Department of Chemistry, University of Alberta, Gunning/Lemieux Chemistry Centre, Edmonton, Alberta T6G 2G2 Canada.
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41
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Papadopoulou MV, Bloomer WD, Rosenzweig HS, Wilkinson SR, Szular J, Kaiser M. Antitrypanosomal activity of 5-nitro-2-aminothiazole-based compounds. Eur J Med Chem 2016; 117:179-86. [PMID: 27092415 PMCID: PMC4876673 DOI: 10.1016/j.ejmech.2016.04.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 12/27/2022]
Abstract
A small series of 5-nitro-2-aminothiazole-based amides containing arylpiperazine-, biphenyl- or aryloxyphenyl groups in their core were synthesized and evaluated as antitrypanosomatid agents. All tested compounds were active or moderately active against Trypanosoma cruzi amastigotes in infected L6 cells and Trypanosoma brucei brucei, four of eleven compounds were moderately active against Leishmania donovani axenic parasites while none were deemed active against T. brucei rhodesiense. For the most active/moderately active compounds a moderate selectivity against each parasite was observed. There was good correlation between lipophilicity (clogP value) and antileishmanial activity or toxicity against L6 cells. Similarly, good correlation existed between clogP values and IC50 values against T. cruzi in structurally related subgroups of compounds. Three compounds were more potent as antichagasic agents than benznidazole but were not activated by the type I nitrorectusase (NTR).
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Affiliation(s)
| | | | | | - Shane R Wilkinson
- School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
| | - Joanna Szular
- School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Parasite Chemotherapy, Basel, Switzerland; University of Basel, Basel, Switzerland
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42
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Predicting human intestinal absorption of diverse chemicals using ensemble learning based QSAR modeling approaches. Comput Biol Chem 2016; 61:178-96. [PMID: 26881740 DOI: 10.1016/j.compbiolchem.2016.01.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 01/18/2016] [Accepted: 01/21/2016] [Indexed: 11/20/2022]
Abstract
Human intestinal absorption (HIA) of the drugs administered through the oral route constitutes an important criterion for the candidate molecules. The computational approach for predicting the HIA of molecules may potentiate the screening of new drugs. In this study, ensemble learning (EL) based qualitative and quantitative structure-activity relationship (SAR) models (gradient boosted tree, GBT and bagged decision tree, BDT) have been established for the binary classification and HIA prediction of the chemicals, using the selected molecular descriptors. The structural diversity of the chemicals and the nonlinear structure in the considered data were tested by the similarity index and Brock-Dechert-Scheinkman statistics. The external predictive power of the developed SAR models was evaluated through the internal and external validation procedures recommended in the literature. All the statistical criteria parameters derived for the performance of the constructed SAR models were above their respective thresholds suggesting for their robustness for future applications. In complete data, the qualitative SAR models rendered classification accuracy of >99%, while the quantitative SAR models yielded correlation (R(2)) of >0.91 between the measured and predicted HIA values. The performances of the EL-based SAR models were also compared with the linear models (linear discriminant analysis, LDA and multiple linear regression, MLR). The GBT and BDT SAR models performed better than the LDA and MLR methods. A comparison of our models with the previously reported QSARs for HIA prediction suggested for their better performance. The results suggest for the appropriateness of the developed SAR models to reliably predict the HIA of structurally diverse chemicals and can serve as useful tools for the initial screening of the molecules in the drug development process.
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43
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Affiliation(s)
- Matthew C T Fyfe
- Topivert Limited, Imperial College Incubator, London, United Kingdom
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44
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Chan MC, Atasoylu O, Hodson E, Tumber A, Leung IKH, Chowdhury R, Gómez-Pérez V, Demetriades M, Rydzik AM, Holt-Martyn J, Tian YM, Bishop T, Claridge TDW, Kawamura A, Pugh CW, Ratcliffe PJ, Schofield CJ. Potent and Selective Triazole-Based Inhibitors of the Hypoxia-Inducible Factor Prolyl-Hydroxylases with Activity in the Murine Brain. PLoS One 2015; 10:e0132004. [PMID: 26147748 PMCID: PMC4492579 DOI: 10.1371/journal.pone.0132004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/09/2015] [Indexed: 01/01/2023] Open
Abstract
As part of the cellular adaptation to limiting oxygen availability in animals, the expression of a large set of genes is activated by the upregulation of the hypoxia-inducible transcription factors (HIFs). Therapeutic activation of the natural human hypoxic response can be achieved by the inhibition of the hypoxia sensors for the HIF system, i.e. the HIF prolyl-hydroxylases (PHDs). Here, we report studies on tricyclic triazole-containing compounds as potent and selective PHD inhibitors which compete with the 2-oxoglutarate co-substrate. One compound (IOX4) induces HIFα in cells and in wildtype mice with marked induction in the brain tissue, revealing that it is useful for studies aimed at validating the upregulation of HIF for treatment of cerebral diseases including stroke.
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Affiliation(s)
- Mun Chiang Chan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Onur Atasoylu
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Emma Hodson
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Anthony Tumber
- Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Ivanhoe K. H. Leung
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Verónica Gómez-Pérez
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Marina Demetriades
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Anna M. Rydzik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - James Holt-Martyn
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Ya-Min Tian
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Tammie Bishop
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Christopher W. Pugh
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Peter J. Ratcliffe
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
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45
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Grädler U, Czodrowski P, Tsaklakidis C, Klein M, Werkmann D, Lindemann S, Maskos K, Leuthner B. Structure-based optimization of non-peptidic Cathepsin D inhibitors. Bioorg Med Chem Lett 2014; 24:4141-50. [PMID: 25086681 DOI: 10.1016/j.bmcl.2014.07.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/15/2014] [Accepted: 07/18/2014] [Indexed: 11/29/2022]
Abstract
We discovered a novel series of non-peptidic acylguanidine inhibitors of Cathepsin D as target for osteoarthritis. The initial HTS-hits were optimized by structure-based design using CatD X-ray structures resulting in single digit nanomolar potency in the biochemical CatD assay. However, the most potent analogues showed only micromolar activities in an ex vivo glycosaminoglycan (GAG) release assay in bovine cartilage together with low cellular permeability and suboptimal microsomal stability. This new scaffold can serve as a starting point for further optimization towards in vivo efficacy.
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Affiliation(s)
- Ulrich Grädler
- Merck KGaA, Merck Serono Research, Small Molecule Platform, Frankfurter Str. 250, 64293 Darmstadt, Germany.
| | - Paul Czodrowski
- Merck KGaA, Merck Serono Research, Small Molecule Platform, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Christos Tsaklakidis
- Merck KGaA, Merck Serono Research, Small Molecule Platform, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Markus Klein
- Merck KGaA, Merck Serono Research, Small Molecule Platform, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Daniela Werkmann
- Merck KGaA, Merck Serono Research, Small Molecule Platform, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Sven Lindemann
- Merck KGaA, Merck Serono Research, Small Molecule Platform, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Klaus Maskos
- Proteros Biostructures GmbH, Bunsenstrasse 7a, 82152 Martinsried, Germany
| | - Birgitta Leuthner
- Merck KGaA, Merck Serono Research, Small Molecule Platform, Frankfurter Str. 250, 64293 Darmstadt, Germany
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46
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Han Y, Zhang JP, Qian JQ, Hu CQ. Cardiotoxicity evaluation of anthracyclines in zebrafish (Danio rerio). J Appl Toxicol 2014; 35:241-52. [PMID: 24853142 DOI: 10.1002/jat.3007] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/12/2014] [Accepted: 02/10/2014] [Indexed: 12/14/2022]
Abstract
Drug-induced cardiotoxicity is a leading factor for drug withdrawals, and limits drug efficacy and clinical use. Therefore, new alternative animal models and methods for drug safety evaluation have been given great attention. Anthracyclines (ANTs) are widely prescribed anticancer agents that have a cumulative dose relationship with cardiotoxicity. We performed experiments to study the toxicity of ANTs in early developing zebrafish embryos, especially their effects on the heart. LC50 values for daunorubicin, pirarubicin, doxorubicin (DOX), epirubicin and DOX-liposome at 72 h post-fertilization were 122.7 μM, 111.9 μM, 31.2 μM, 108.3 μM and 55.8 μM, respectively. At the same time, zebrafish embryos were exposed to ANTs in three exposure stages and induced incomplete looping of the heart tube, pericardia edema and bradycardia in a dose-dependent manner, eventually leading to death. DOX caused the greatest heart defects in the treatment stages and its liposome reduced the effects on the heart, while daunorubicin produced the least toxicity. Genes and proteins related to heart development were also identified to be sensitive to ANT exposure and downregulated by ANTs. It revealed ANTs could disturb the heart formation and development. ANTs induced cardiotoxicity in zebrafish has similar effects in mammalian models, indicating that zebrafish may have a potential value for assessment of drug-induced developmental cardiotoxicity.
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Affiliation(s)
- Ying Han
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
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47
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Grädler U, Bomke J, Musil D, Dresing V, Lehmann M, Hölzemann G, Greiner H, Esdar C, Krier M, Heinrich T. Fragment-based discovery of focal adhesion kinase inhibitors. Bioorg Med Chem Lett 2013; 23:5401-9. [DOI: 10.1016/j.bmcl.2013.07.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/17/2013] [Accepted: 07/23/2013] [Indexed: 12/14/2022]
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48
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Zhang J, Qian J, Tong J, Zhang D, Hu C. Toxic Effects of Cephalosporins with Specific Functional Groups as Indicated by Zebrafish Embryo Toxicity Testing. Chem Res Toxicol 2013; 26:1168-81. [DOI: 10.1021/tx400089y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jingpu Zhang
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianqin Qian
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- National Institutes for Food and Drug Control, Beijing, China
| | - Junwei Tong
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Dousheng Zhang
- National Institutes for Food and Drug Control, Beijing, China
| | - Changqin Hu
- National Institutes for Food and Drug Control, Beijing, China
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49
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Vistoli G, De Maddis D, Straniero V, Pedretti A, Pallavicini M, Valoti E, Carini M, Testa B, Aldini G. Exploring the space of histidine containing dipeptides in search of novel efficient RCS sequestering agents. Eur J Med Chem 2013; 66:153-60. [PMID: 23792353 DOI: 10.1016/j.ejmech.2013.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 02/25/2013] [Accepted: 05/10/2013] [Indexed: 11/16/2022]
Abstract
The study reports a set of forty proteinogenic histidine-containing dipeptides as potential carbonyl quenchers. The peptides were chosen to cover as exhaustively as possible the accessible chemical space, and their quenching activities toward 4-hydroxy-2-nonenal (HNE) and pyridoxal were evaluated by HPLC analyses. The peptides were capped at the C-terminus as methyl esters or amides to favor their resistance to proteolysis and diastereoisomeric pairs were considered to reveal the influence of configuration on quenching. On average, the examined dipeptides are less active than the parent compound carnosine (βAla + His) thus emphasizing the unfavorable effect of the shortening of the βAla residue as confirmed by the control dipeptide Gly-His. Nevertheless, some peptides show promising activities toward HNE combined with a remarkable selectivity. The results emphasize the beneficial role of aromatic and positively charged residues, while negatively charged and H-bonding side chains show a detrimental effect on quenching. As a trend, ester derivatives are slightly more active than amides while heterochiral peptides are more active than their homochiral diastereoisomer. Overall, the results reveal that quenching activity strongly depends on conformational effects and vicinal residues (as evidenced by the reported QSAR analysis), offering insightful clues for the design of improved carbonyl quenchers and to rationalize the specific reactivity of histidine residues within proteins.
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Affiliation(s)
- Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy.
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50
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Costache MC, Vaughan AD, Qu H, Ducheyne P, Devore DI. Tyrosine-derived polycarbonate-silica xerogel nanocomposites for controlled drug delivery. Acta Biomater 2013; 9:6544-52. [PMID: 23395749 DOI: 10.1016/j.actbio.2013.01.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 01/14/2013] [Accepted: 01/29/2013] [Indexed: 11/29/2022]
Abstract
Biodegradable polymer-ceramic composites offer significant potential advantages in biomedical applications where the properties of either polymers or ceramics alone are insufficient to meet performance requirements. Here we demonstrate the highly tunable mechanical and controlled drug delivery properties accessible with novel biodegradable nanocomposites prepared by non-covalent binding of silica xerogels and co-polymers of tyrosine-poly(ethylene glycol)-derived poly(ether carbonate). The Young's moduli of the nanocomposites exceed by factors of 5-20 times those of the co-polymers or of composites made with micron scale silica particles. Increasing the fraction of xerogel in the nanocomposites increases the glass transition temperature and the mechanical strength, but decreases the equilibrium water content, which are all indicative of strong non-covalent interfacial interactions between the co-polymers and the silica nanoparticles. Sustained, tunable controlled release of both hydrophilic and hydrophobic therapeutic agents from the nanocomposites is demonstrated with two clinically significant drugs, rifampicin and bupivacaine. Bupivacaine exhibits an initial small burst release followed by slow release over the 7 day test period. Rifampicin release fits the diffusion-controlled Higuchi model and the amount released exceeds the dosage required for treatment of clinically challenging infections. These nanocomposites are thus attractive biomaterials for applications such as wound dressings, tissue engineering substrates and stents.
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Affiliation(s)
- M C Costache
- New Jersey Center for Biomaterials, Rutgers-The State University of New Jersey, Piscataway, NJ 08854, USA
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