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Samizo S, Kaneko H. Predictive Modeling of HMG-CoA Reductase Inhibitory Activity and Design of New HMG-CoA Reductase Inhibitors. ACS OMEGA 2023; 8:27247-27255. [PMID: 37546661 PMCID: PMC10399166 DOI: 10.1021/acsomega.3c02567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/30/2023] [Indexed: 08/08/2023]
Abstract
As blood cholesterol increases, it accumulates in the intima of blood vessels, elevating the risk of atherosclerosis and coronary artery disease. Drugs that inhibit enzymes essential for cholesterol synthesis are effective in improving blood cholesterol levels. Statins are used to treat hypercholesterolemia as they inhibit 3-hydroxyl-3-methylglutaryl coenzyme A (HMG-CoA) reductase (HMGR), the rate-limiting enzyme in cholesterol synthesis. Statins are known to exert their effects by translocating to the liver, where they are taken up by the organic anion transporting polypeptide 1B1 (OATP1B1). Therefore, we hypothesized that a compound with high HMGR inhibitory activity and high affinity for OATP1B1 would be an excellent new therapeutic agent for hypercholesterolemia with increased liver selectivity and fewer side effects. In this study, we developed two models for predicting HMGR inhibitory activity and OATP1B1 affinity to propose the chemical structure of a new therapeutic agent for hypercholesterolemia with both high inhibitory activity and high liver selectivity. HMGR inhibitory activity and OATP1B1 affinity prediction models were constructed with high prediction accuracy for the test data: r2 = 0.772 and 0.768, respectively. New chemical structures were then input into these models to search for candidate compounds. We found compounds with higher HMGR inhibitory activity and OATP1B1 affinity than rosuvastatin, the most recently developed statin drug, and compounds that did not have a common structure of statins with high HMGR inhibitory activity.
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Computer-Aided and AILDE Approaches to Design Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors. Int J Mol Sci 2022; 23:ijms23147822. [PMID: 35887168 PMCID: PMC9320391 DOI: 10.3390/ijms23147822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 01/19/2023] Open
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a pivotal enzyme in tocopherol and plastoquinone synthesis and a potential target for novel herbicides. Thirty-five pyridine derivatives were selected to establish a Topomer comparative molecular field analysis (Topomer CoMFA) model to obtain correlation information between HPPD inhibitory activity and the molecular structure. A credible and predictive Topomer CoMFA model was established by "split in two R-groups" cutting methods and fragment combinations (q2 = 0.703, r2 = 0.957, ONC = 6). The established model was used to screen out more active compounds and was optimized through the auto in silico ligand directing evolution (AILDE) platform to obtain potential HPPD inhibitors. Twenty-two new compounds with theoretically good HPPD inhibition were obtained by combining the high-activity contribution substituents in the existing molecules with the R-group search via Topomer search. Molecular docking results revealed that most of the 22 fresh compounds could form stable π-π interactions. The absorption, distribution, metabolism, excretion and toxicity (ADMET) prediction and drug-like properties made 9 compounds potential HPPD inhibitors. Molecular dynamics simulation indicated that Compounds Y12 and Y14 showed good root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values and stability. According to the AILDE online verification, 5 new compounds with potential HPPD inhibition were discovered as HPPD inhibitor candidates. This study provides beneficial insights for subsequent HPPD inhibitor design.
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Significance of stressor media on the stability of statins: a critical assessment. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02306-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Shao N, Liu X, Monnier V, Charles L, Rodriguez J, Bressy C, Quintard A. Enantioselective Synthesis of Acyclic Stereotriads Featuring Fluorinated Tetrasubstituted Stereocenters. Chemistry 2021; 28:e202103874. [PMID: 34821417 DOI: 10.1002/chem.202103874] [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: 10/27/2021] [Indexed: 11/07/2022]
Abstract
Elaboration of enantioenriched complex acyclic stereotriads represents a challenge for modern synthesis even more when fluorinated tetrasubstituted stereocenters are targeted. We have been able to develop a simple strategy in a sequence of two unprecedented steps combining a diastereoselective aldol-Tishchenko reaction and an enantioselective organocatalyzed kinetic resolution. The aldol-Tishchenko reaction directly generates a large panel of acyclic 1,3-diols possessing a fluorinated tetrasubstituted stereocenter by condensation of fluorinated ketones with aldehydes under very mild basic conditions. The anti 1,3-diols featuring three contiguous stereogenic centers are generated with excellent diastereocontrol (typically >99 : 1 dr). Depending upon the precursors both diastereomers of stereotriads are accessible through this flexible reaction. Furthermore, from the obtained racemic scaffolds, development of an organocatalyzed kinetic resolution enabled to generate the desired enantioenriched stereotriads with excellent selectivity (typically er >95 : 5).
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Affiliation(s)
- Na Shao
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Xueyang Liu
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Valérie Monnier
- Aix Marseille Univ, CNRS, Centrale Marseille, FSCM, Marseille, France
| | | | - Jean Rodriguez
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Cyril Bressy
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Adrien Quintard
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
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Desrues T, Merad J, Andrei D, Pons J, Parrain J, Médebielle M, Quintard A, Bressy C. Impact of the Difluoromethylene Group in the Organocatalyzed Acylative Kinetic Resolution of α,α‐Difluorohydrins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Titouan Desrues
- Aix-Marseille Univ CNRS Centrale Marseille, iSm2 Marseille France
| | - Jérémy Merad
- Univ Lyon Université Lyon 1 CNRS INSA CPE-Lyon ICBMS UMR 5246 Bât. Lederer 1 rue Victor Grignard 69622 Villeurbanne France
| | - Daniela Andrei
- Univ Lyon Université Lyon 1 CNRS INSA CPE-Lyon ICBMS UMR 5246 Bât. Lederer 1 rue Victor Grignard 69622 Villeurbanne France
- Dominican University 7900 West Division Street River Forest IL 60305 USA
| | - Jean‐Marc Pons
- Aix-Marseille Univ CNRS Centrale Marseille, iSm2 Marseille France
| | - Jean‐Luc Parrain
- Aix-Marseille Univ CNRS Centrale Marseille, iSm2 Marseille France
| | - Maurice Médebielle
- Univ Lyon Université Lyon 1 CNRS INSA CPE-Lyon ICBMS UMR 5246 Bât. Lederer 1 rue Victor Grignard 69622 Villeurbanne France
| | - Adrien Quintard
- Aix-Marseille Univ CNRS Centrale Marseille, iSm2 Marseille France
| | - Cyril Bressy
- Aix-Marseille Univ CNRS Centrale Marseille, iSm2 Marseille France
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Desrues T, Merad J, Andrei D, Pons JM, Parrain JL, Médebielle M, Quintard A, Bressy C. Impact of the Difluoromethylene Group in the Organocatalyzed Acylative Kinetic Resolution of α,α-Difluorohydrins. Angew Chem Int Ed Engl 2021; 60:24924-24929. [PMID: 34473886 DOI: 10.1002/anie.202107041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 12/15/2022]
Abstract
Due to the omnipresence of chiral organofluorine compounds in pharmaceutical, agrochemical, and material chemistry, the development of enantioselective methods for their preparation is highly desirable. In the present study, the enantioselective organocatalyzed acylation of α,α-difluorohydrins using a commercially available chiral isothiourea is reported through a kinetic resolution (KR) process. It reveals that the difluoromethylene moiety (C(sp3 )F2 ) can serve as a directing group through electrostatic fluorine-cation interactions, greatly improving the enantioselectivity of the KR. In this context, a broad range of fluorinated alcohols such as valuable 4,4-difluoro-1,3-diols could be synthesized with exquisite enantiocontrol (typically >99:1 er). Turning to 2,2-difluoro-1,3-diols, we also demonstrated that aromatic and fluorinated groups were mutually compatible to provide the expected enantioenriched adducts with >99:1 er.
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Affiliation(s)
- Titouan Desrues
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Jérémy Merad
- Univ Lyon, Université Lyon 1, CNRS, INSA, CPE-Lyon, ICBMS, UMR 5246, Bât. Lederer, 1 rue Victor Grignard, 69622, Villeurbanne, France
| | - Daniela Andrei
- Univ Lyon, Université Lyon 1, CNRS, INSA, CPE-Lyon, ICBMS, UMR 5246, Bât. Lederer, 1 rue Victor Grignard, 69622, Villeurbanne, France.,Dominican University, 7900 West Division Street, River Forest, IL, 60305, USA
| | - Jean-Marc Pons
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Jean-Luc Parrain
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Maurice Médebielle
- Univ Lyon, Université Lyon 1, CNRS, INSA, CPE-Lyon, ICBMS, UMR 5246, Bât. Lederer, 1 rue Victor Grignard, 69622, Villeurbanne, France
| | - Adrien Quintard
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Cyril Bressy
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
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Qureshi S, Khandelwal R, Madhavi M, Khurana N, Gupta N, Choudhary SK, Suresh RA, Hazarika L, Srija CD, Sharma K, Hindala MR, Hussain T, Nayarisseri A, Singh SK. A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma. Curr Top Med Chem 2021; 21:790-818. [PMID: 33463471 DOI: 10.2174/1568026621666210119112336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32). AIM The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL. METHODOLOGY Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds. RESULT MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies. CONCLUSION Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.
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Affiliation(s)
- Shahrukh Qureshi
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad - 500001, Telangana State, India
| | - Naveesha Khurana
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Neha Gupta
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Saurav K Choudhary
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Revathy A Suresh
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Lima Hazarika
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Chillamcherla D Srija
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Mali R Hindala
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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Abdizadeh R, Heidarian E, Hadizadeh F, Abdizadeh T. QSAR Modeling, Molecular Docking and Molecular Dynamics Simulations Studies of Lysine-Specific Demethylase 1 (LSD1) Inhibitors as Anticancer Agents. Anticancer Agents Med Chem 2021; 21:987-1018. [PMID: 32698753 DOI: 10.2174/1871520620666200721134010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/07/2020] [Accepted: 05/17/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Histone Lysine Demetylases1 (LSD1) is a promising medication to treat cancer, which plays a crucial role in epigenetic modulation of gene expression. Inhibition of LSD1with small molecules has emerged as a vital mechanism to treat cancer. OBJECTIVE In the present research, molecular modeling investigations, such as CoMFA, CoMFA-RF, CoMSIA and HQSAR, molecular docking and Molecular Dynamics (MD) simulations were carried out on some tranylcypromine derivatives as LSD1 inhibitors. METHODS The QSAR models were carried out on a series of Tranylcypromine derivatives as data set via the SYBYL-X2.1.1 program. Molecular docking and MD simulations were carried out by the MOE software and the SYBYL program, respectively. The internal and external predictability performances related to the generated models for these LSD1 inhibitors were justified by evaluating cross-validated correlation coefficient (q2), noncross- validated correlation coefficient (r2ncv) and predicted correlation coefficient (r2pred) of the training and test set molecules, respectively. RESULTS The CoMFA (q2, 0.670; r2ncv, 0.930; r2pred, 0.968), CoMFA-RF (q2, 0.694; r2ncr, 0.926; r2pred, 0.927), CoMSIA (q2, 0.834; r2ncv, 0.956; r2pred, 0.958) and HQSAR models (q2, 0.854; r2ncv, 0.900; r2pred, 0.728) for training as well as the test set of LSD1 inhibition resulted in significant findings. CONCLUSION These QSAR models were found to be perfect and strong with better predictability. Contour maps of all models were generated and it was proven by molecular docking studies and molecular dynamics simulation that the hydrophobic, electrostatic and hydrogen bonding fields are crucial in these models for improving the binding affinity and determining the structure-activity relationship. These theoretical results are possibly beneficial to design new strong LSD1 inhibitors with enhanced activity to treat cancer.
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Affiliation(s)
- Rahman Abdizadeh
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Esfandiar Heidarian
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Sharekord University of Medical Sciences, Shahrekord, Iran
| | - Farzin Hadizadeh
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tooba Abdizadeh
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Sharekord University of Medical Sciences, Shahrekord, Iran
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Alnajjar R, Mohamed N, Kawafi N. Bicyclo[1.1.1]Pentane as Phenyl Substituent in Atorvastatin Drug to improve Physicochemical Properties: Drug-likeness, DFT, Pharmacokinetics, Docking, and Molecular Dynamic Simulation. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Quintard A. Copper Catalyzed Decarboxylative Functionalization of Ketoacids. CHEM REC 2021; 21:3382-3393. [PMID: 33750015 DOI: 10.1002/tcr.202100045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/30/2022]
Abstract
Selective copper catalyzed activation of ketoacids and notably bio-sourced 1,3-acetonedicarboxylic acid, represents an attractive strategy to solve key synthetic challenges. Condensation with aldehydes under exceedingly mild conditions can create more rapidly known natural products scaffolds such as 1,3 polyols. In this account, the recent progress in this field, notably through multicatalytic combination with organocatalysis is described. In addition to the rapid preparation of natural product fragments, cascade incorporation of fluorine also provided new type of synthetic analogues of improved properties in a broad range of applications.
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Affiliation(s)
- Adrien Quintard
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
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Panigrahi D, Mishra A, Sahu SK, Azam MA, Vyshaag CM. A Combined approach of Pharmacophore Modeling, QSAR Study, Molecular Docking and in silico ADME/Tox prediction of 4-Arylthio & 4- Aryloxy-3- Iodopyridine-2(1H)-one analogs to identify potential Reverse Transcriptase inhibitor: Anti-HIV agents. Med Chem 2020; 18:51-87. [PMID: 33319692 DOI: 10.2174/1573406417666201214100822] [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: 05/01/2020] [Revised: 08/31/2020] [Accepted: 10/12/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Reverse transcriptase is an important therapeutic target to treat AIDS caused by the Human Immunodeficiency Virus (HIV). Despite many effective anti-HIV drugs, reverse transcriptase (RT) inhibitors remain the cornerstone of the drug regimen to treat AIDS. In the present work, we have expedited the use of different computational modules and presented an easy, cost-effective and high throughput screening method to identify potential reverse transcriptase inhibitors. METHODS A congeneric series of 4-Arylthio & 4-Aryloxy-3- Iodopyridine-2(1H)-one analogs having anti-HIV activity were subjected to structure-based 2D, 3D QSAR, Pharmacophore Modeling, and Molecular Docking to elucidate the structural properties required for the design of potent HIV-RT inhibitors. Prediction of preliminary Pharmacokinetic and the Drug Likeliness profile was performed for these compounds by in silico ADME study. RESULTS The 2D and 3D- QSAR models were developed by correlating two and three-dimensional descriptors with activity (pIC50) by sphere exclusion method and k-nearest neighbor molecular field analysis approach, respectively. The significant 2D- QSAR model developed by Partial Least Square associated with the Sphere Exclusion method (PLS-SE) having r2 and q2 values 0.9509 and 0.8038 respectively. The 3D-QSAR model by Step Wise variable selection method (SW-kNN MFA) is more significant which has a cross-validated squared correlation coefficient q2= 0.8509 and a non-cross-validated correlation coefficient pred_r2= 0.8102. The pharmacophore hypothesis was developed which comprised 5 features includes 3 aliphatic regions (Ala), 1 H-bond donor (HDr) and 1 H-bond acceptor (HAc). Docking studies of the selected inhibitors with the active site of reverse transcriptase enzyme showed hydrogen bond and π - π interaction with LYS-101, LYS-103, TYR- 181, TYR-188 and TRP-229 residues present at the active site. All the candidates with good bioavailability and ADMET drug likeliness properties. CONCLUSION The results of the present work provide more useful information and important structural insights for the discovery, design of novel and potent reverse transcriptase inhibitors with high therapeutic windows in the future.
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Affiliation(s)
- Debadash Panigrahi
- Drug Research Laboratory, Nodal Research Centre, College of Pharmaceutical Sciences, Puri, Baliguali, Puri- Konark Marine Drive road, Puri, Odisha. India
| | - Amiyakanta Mishra
- Drug Research Laboratory, Nodal Research Centre, College of Pharmaceutical Sciences, Puri, Baliguali, Puri- Konark Marine Drive road, Puri, Odisha. India
| | - Susanta Kumar Sahu
- Dept. of Pharmacy, Utkal University, VaniVihar, Bhubaneswar, Odisha. India
| | - Mohd Afzal Azam
- Dept. of Pharmaceutical Chemistry, J.S.S. College of Pharmacy, Ooty, Udhagamandalam, Tamil Nadu. India
| | - C M Vyshaag
- Dept. of Pharmaceutical Chemistry, J.S.S. College of Pharmacy, Ooty, Udhagamandalam, Tamil Nadu. India
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Panigrahi D, Mishra A, Sahu SK. Rational in silico drug design of HIV-RT inhibitors through G-QSAR and molecular docking study of 4-arylthio and 4-aryloxy-3-iodopyridine-2(1-H)-one derivative. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2020. [DOI: 10.1186/s43088-020-00075-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Human immunodeficiency virus infection and acquired immune deficiency syndrome (HIV/AIDS) is a spectrum of conditions caused by infection with the human immunodeficiency virus (HIV). Antiretroviral therapy (ART) against HIV infection offers the promise of controlling disease progression and prolonging the survival of HIV-infected patients. Reverse transcriptase (RT) inhibitors remain the cornerstone of the drug regimen to treat AIDS. In this direction, by using group-based QSAR study (G-QSAR), identification of the structural need for the development of lead structure with reverse transcriptase inhibition on 97 reported structures was carried out. Docking analysis was performed further and suggested the structural properties required for binding affinity with the receptor. The molecules in the data set were fragmented into six (R1, R2, R3, R4, R5, and R6) by applying the fragmentation pattern. Three G-QSAR models were selected based on the statistical significance of the model. The molecular docking study was performed to explain the structural properties required for the design of potent HIV-RT inhibitors.
Results
The statistically validated QSAR models reveal the presence of higher hydrophobic groups containing single-bonded –Br atom, 2 aromatic bonded –NH group with less electronegativity, and entropic interaction fields at R2 essential for better anti-HIV activity. The presence of a lipophilic group at R3, oxygen and sulfur connected with two aromatic bonds at R4, and –CH3 group at R5 was fruitful for reverse transcriptase inhibition. Docking studies of the selected inhibitors with the active site of reverse transcriptase enzyme showed hydrogen bond, Van der Waal’s, charge, aromatic, and π–π interactions with residues present at the active site.
Conclusion
The results of the generated models provide significant site-specific insight into the structural requirements for reverse transcriptase inhibition during the design and development of novel anti-HIV compounds. Molecular docking study revealed the binding interaction between the ligand and the receptor which gave insight towards the structure-based design for the discovery of more potent compounds with better activity against HIV infection.
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Abdizadeh R, Heidarian E, Hadizadeh F, Abdizadeh T. Investigation of pyrimidine analogues as xanthine oxidase inhibitors to treat of hyperuricemia and gout through combined QSAR techniques, molecular docking and molecular dynamics simulations. J Taiwan Inst Chem Eng 2020. [DOI: 10.1016/j.jtice.2020.08.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Pharmacophore modelling, QSAR study, molecular docking and insilico ADME prediction of 1,2,3-triazole and pyrazolopyridones as DprE1 inhibitor antitubercular agents. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2638-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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In silico studies of novel scaffold of thiazolidin-4-one derivatives as anti-Toxoplasma gondii agents by 2D/3D-QSAR, molecular docking, and molecular dynamics simulations. Struct Chem 2020. [DOI: 10.1007/s11224-019-01458-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Guo P, Zhang R, Wang X, Wang Z, Ding K. Synthesis of Chiral Tertiary α,α‐Difluoromethyl Carbinols by Cu‐Catalyzed Asymmetric Propargylation. Chemistry 2019; 25:16425-16434. [DOI: 10.1002/chem.201904543] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Peihua Guo
- State Key Laboratory of Organometallic ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryChinese Academy of Sciences 345 Lingling Road Shanghai 200032 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Rui Zhang
- State Key Laboratory of Organometallic ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryChinese Academy of Sciences 345 Lingling Road Shanghai 200032 P. R. China
| | - Xiaoming Wang
- State Key Laboratory of Organometallic ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryChinese Academy of Sciences 345 Lingling Road Shanghai 200032 P. R. China
| | - Zheng Wang
- State Key Laboratory of Organometallic ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryChinese Academy of Sciences 345 Lingling Road Shanghai 200032 P. R. China
| | - Kuiling Ding
- State Key Laboratory of Organometallic ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryChinese Academy of Sciences 345 Lingling Road Shanghai 200032 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Collaborative Innovation Center of Chemical Science and EngineeringNankai University Tianjin 300071 P. R. China
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17
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Safarizadeh H, Garkani-Nejad Z. Molecular docking, molecular dynamics simulations and QSAR studies on some of 2-arylethenylquinoline derivatives for inhibition of Alzheimer's amyloid-beta aggregation: Insight into mechanism of interactions and parameters for design of new inhibitors. J Mol Graph Model 2019; 87:129-143. [DOI: 10.1016/j.jmgm.2018.11.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 11/18/2018] [Accepted: 11/30/2018] [Indexed: 02/06/2023]
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18
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Safarizadeh H, Garkani-Nejad Z. Investigation of MI-2 analogues as MALT1 inhibitors to treat of diffuse large B-Cell lymphoma through combined molecular dynamics simulation, molecular docking and QSAR techniques and design of new inhibitors. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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19
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Design, synthesis and biological evaluation of novel zanamivir derivatives as potent neuraminidase inhibitors. Bioorg Med Chem Lett 2018; 28:3622-3629. [PMID: 30389293 DOI: 10.1016/j.bmcl.2018.10.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/25/2018] [Indexed: 01/22/2023]
Abstract
Neuraminidase (NA) is an important antiviral drug target. Zanamivir is one of the most potent NA inhibitors. In this paper, a series of zanamivir derivatives as potential NA inhibitors were studied by combination of molecular modeling techniques including 3D-QSAR, molecular docking, and molecular dynamics (MD) simulation. The results show that the best CoMFA (comparative molecular field analysis) model has q2 = 0.728 and r2 = 0.988, and the best CoMSIA (comparative molecular similarity indices analysis) model has q2 = 0.750 and r2 = 0.981, respectively. The built 3D-QSAR models show significant statistical quality and excellent predictive ability. Seven new NA inhibitors were designed and predicted. 20 ns of MD simulations were carried out and their binding free energies were calculated. Two designed compounds were selected to be synthesized and biologically evaluated by NA inhibition and virus inhibition assays. One compound (IC50 = 0.670 µM, SI > 149) exhibits excellent antiviral activity against A/WSN/33 H1N1, which is superior to the reference drug zanamivir (IC50 = 0.873 µM, SI > 115). The theoretical and experimental results may provide reference for development of new anti-influenza drugs.
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20
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Pandit A, Sengupta S, Krishnan MA, Reddy RB, Sharma R, Venkatesh C. First report on 3D-QSAR and molecular dynamics based docking studies of GCPII inhibitors for targeted drug delivery applications. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Ricucci A, Rodriguez J, Quintard A. Organo- and Copper-Multi-Catalyzed Pseudo Four-Component Access to gem
-Difluorohydrins. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701459] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Angela Ricucci
- CNRS, Centrale Marseille, iSm2; Aix Marseille Université; 13397 Marseille France
| | - Jean Rodriguez
- CNRS, Centrale Marseille, iSm2; Aix Marseille Université; 13397 Marseille France
| | - Adrien Quintard
- CNRS, Centrale Marseille, iSm2; Aix Marseille Université; 13397 Marseille France
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22
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Design, synthesis and biological evaluation of novel oseltamivir derivatives as potent neuraminidase inhibitors. Bioorg Med Chem Lett 2017; 27:5429-5435. [DOI: 10.1016/j.bmcl.2017.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 10/27/2017] [Accepted: 11/02/2017] [Indexed: 11/19/2022]
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23
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Quintard A, Rodriguez J. Bicatalyzed Three-Component Stereoselective Decarboxylative Fluoro-Aldolization for the Construction of Elongated Fluorohydrins. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02353] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Adrien Quintard
- Aix Marseille Univ, CNRS, Centrale Marseille,
iSm2, Marseille, 13397, France
| | - Jean Rodriguez
- Aix Marseille Univ, CNRS, Centrale Marseille,
iSm2, Marseille, 13397, France
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24
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Gao X, Han L, Ren Y. In Silico Exploration of 1,7-Diazacarbazole Analogs as Checkpoint Kinase 1 Inhibitors by Using 3D QSAR, Molecular Docking Study, and Molecular Dynamics Simulations. Molecules 2016; 21:molecules21050591. [PMID: 27164065 PMCID: PMC6273173 DOI: 10.3390/molecules21050591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 04/11/2016] [Accepted: 04/28/2016] [Indexed: 12/11/2022] Open
Abstract
Checkpoint kinase 1 (Chk1) is an important serine/threonine kinase with a self-protection function. The combination of Chk1 inhibitors and anti-cancer drugs can enhance the selectivity of tumor therapy. In this work, a set of 1,7-diazacarbazole analogs were identified as potent Chk1 inhibitors through a series of computer-aided drug design processes, including three-dimensional quantitative structure–activity relationship (3D-QSAR) modeling, molecular docking, and molecular dynamics simulations. The optimal QSAR models showed significant cross-validated correlation q2 values (0.531, 0.726), fitted correlation r2 coefficients (higher than 0.90), and standard error of prediction (less than 0.250). These results suggested that the developed models possess good predictive ability. Moreover, molecular docking and molecular dynamics simulations were applied to highlight the important interactions between the ligand and the Chk1 receptor protein. This study shows that hydrogen bonding and electrostatic forces are key interactions that confer bioactivity.
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Affiliation(s)
- Xiaodong Gao
- School of Chemistry and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
| | - Liping Han
- School of Chemistry and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
| | - Yujie Ren
- School of Chemistry and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
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25
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3D-QSAR, molecular dynamics simulations and molecular docking studies of benzoxazepine moiety as mTOR inhibitor for the treatment of lung cancer. Bioorg Med Chem Lett 2016; 26:864-874. [DOI: 10.1016/j.bmcl.2015.12.075] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/07/2015] [Accepted: 12/22/2015] [Indexed: 01/18/2023]
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26
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Saadi J, Wennemers H. Enantioselective aldol reactions with masked fluoroacetates. Nat Chem 2016; 8:276-80. [DOI: 10.1038/nchem.2437] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/07/2015] [Indexed: 12/23/2022]
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27
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Pharmacodynamics and potential synergistic effects of Mai-Luo-Ning injection on cardiovascular protection, based on molecular docking. Chin J Nat Med 2015; 13:815-822. [PMID: 26614456 DOI: 10.1016/s1875-5364(15)30085-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 11/20/2022]
Abstract
As a computer-assisted approach, molecular docking has been universally applied in drug research and development and plays an important role in the investigation and evaluation of herbal medicines. Herein, the method was used to estimate the pharmacodynamics of Mai-Luo-Ning injection, a traditional Chinese compound herbal prescription. Through investigating the interactions between several important proteins in cardiovascular system and characteristic components of the formula, its effect on cardiovascular protection was evaluated. Results showed the differences in the interactions between each component and the selected target proteins and revealed the possible mechanisms for synergistic effects of various characteristic components on cardiovascular protection. The study provided scientific evidence supporting the mechanistic study of the interactions among multi-components and targets, offering a general approach to investigating the pharmacodynamics of complicated materials in compound herbal prescriptions.
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28
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Synthesis, antiviral activity, 3D-QSAR, and interaction mechanisms study of novel malonate derivatives containing quinazolin-4(3H)-one moiety. Bioorg Med Chem Lett 2015; 26:168-73. [PMID: 26598463 DOI: 10.1016/j.bmcl.2015.11.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/28/2015] [Accepted: 11/04/2015] [Indexed: 11/22/2022]
Abstract
A series of novel malonate derivatives containing quinazolin-4(3H)-one moiety were synthesized and evaluated for their antiviral activities against cucumber mosaic virus (CMV). Results indicated that the title compounds exhibited good antiviral activities. Notably, compounds g15, g16, g17, and g18 exhibited excellent curative activities in vivo against CMV, with 50% effective concentration (EC50) values of 208.36, 153.78, 181.47, and 164.72μg/mL, respectively, which were better than that of Ningnanmycin (256.35μg/mL) and Ribavirin (523.34μg/mL). Moreover, statistically valid three-dimensional quantitative structure-activity relationship (3D-QSAR) models with good correlation and predictive power were obtained with comparative molecular field analysis (CoMFA) steric and electrostatic fields (r(2)=0.990, q(2)=0.577) and comparative molecular similarity indices analysis (CoMSIA) with combined steric, electrostatic, hydrophobic and hydrogen bond acceptor fields (r(2)=0.977, q(2)=0.516), respectively. Based on those models, compound g25 was designed, synthesized, and showed better curative activity (146.30μg/mL) than that of compound g16. The interaction of between cucumber mosaic virus coat protein (CMV CP) and g25 with 1:1.83 ratio is typically spontaneous and exothermic with micromole binding affinity by isothermal titration calorimetry (ITC) and fluorescence spectroscopy investigation.
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29
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Xu C, Ren Y. Molecular modeling studies of [6,6,5] Tricyclic Fused Oxazolidinones as FXa inhibitors using 3D-QSAR, Topomer CoMFA, molecular docking and molecular dynamics simulations. Bioorg Med Chem Lett 2015; 25:4522-8. [PMID: 26343829 DOI: 10.1016/j.bmcl.2015.08.070] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/22/2015] [Accepted: 08/26/2015] [Indexed: 10/23/2022]
Abstract
Coagulation factor Xa (Factor Xa, FXa) is a particularly promising target for novel anticoagulant therapy. The first oral factor Xa inhibitor has been approved in the EU and Canada in 2008. In this work, 38 [6,6,5] Tricyclic Fused Oxazolidinones were studied using a combination of molecular modeling techniques including three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, molecular dynamics and Topomer CoMFA (comparative molecular field analysis) were used to build 3D-QSAR models. The results show that the best CoMFA model has q(2)=0.511 and r(2)=0.984, the best CoMSIA (comparative molecular similarity indices analysis) model has q(2)=0.700 and r(2)=0.993 and the Topomer CoMFA analysis has q(2)=0.377 and r(2)=0.886. The results indicated the steric, hydrophobic, H-acceptor and electrostatic fields play key roles in models. Molecular docking and molecular dynamics explored the binding relationship of the ligand and the receptor protein.
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Affiliation(s)
- Cheng Xu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Yujie Ren
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
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