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Upadhyaya A, Panthi B, Verma S, Kumar S, Rajouria SK, Srivastava HK, Chandra P. Analogue and structure based approaches for modelling HIV-1 integrase inhibitors. J Biomol Struct Dyn 2023; 41:11946-11956. [PMID: 36734646 DOI: 10.1080/07391102.2023.2171129] [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: 05/27/2021] [Accepted: 12/25/2022] [Indexed: 02/04/2023]
Abstract
A set of 220 inhibitors belonging to different structure classes and having HIV-1 integrase activity were collected along with their experimental pIC50 values. Geometries of all the inhibitors were fully optimized using B3LYP/6-31 + G(d) level of theory. These ligands were docked against 4 different HIV-1 integrase receptors (PDB IDs: 4LH5, 5KRS, 3ZSQ and 3ZSV). 30 docked poses were generated for all 220 inhibitors and ligand interaction of the first docked pose and the docked pose with the highest score were analysed. Residue GLU170 of 4LH5 receptor shows the highest number of interactions followed by ALA169, GLN168, HIS171 and ASP167 residues. Hydrogen bonding and stacking are mainly responsible for the interactions of these inhibitors with the receptor. We performed Molecular Dynamics (MD) simulation to observe the root-mean-square deviation (RMSD), for measure the average change of displacement between the atoms for a particular frame with respect to a reference and The Root Mean Square Fluctuation (RMSF) for characterization of local changes along the protein chain of the docked complexes. Analogue based models were generated to predict the pIC50 values for integrase inhibitors using various types of descriptors such as constitutional, geometrical, topological, quantum chemical and docking based descriptors. The best models were selected on the basis of statistical parameters and were validated by training and test set division. A few new inhibitors were designed on the basis of structure activity relationship and their pIC50 values were predicted using the generated models. All the designed new inhibitors a very high potential and may be used as potent inhibitors of HIV integrase. These models may be useful for further design and development of new and potent HIV integrase inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anurag Upadhyaya
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Bhavana Panthi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kalyanpur Kanpur, Uttar Pradesh, India
| | - Shubham Verma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Changsari, Guwahati, Assam, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Suresh Kumar
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- Department of Physics, Dyal Singh College, University of Delhi, Delhi, India
| | - Satish Kumar Rajouria
- Department of Physics, Zakir Husain Delhi College, University of Delhi, Delhi, India
| | - Hemant Kumar Srivastava
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Changsari, Guwahati, Assam, India
| | - Pranjal Chandra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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Wu Y, Cao C, Yuan H. Estimation of the ionization potential for polyhalogenated hydrocarbons by weakest bound potential method. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1879] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yaxin Wu
- School of Chemistry and Chemical Engineering; Central South University; Changsha 410083 China
- School of Chemistry and Chemical Engineering; Hunan University of Science and Technology; Xiangtan 411201 China
- Key Laboratory of Theoretical Chemistry and Molecular Simulation of Ministry of Education; Hunan University of Science and Technology; China
- Hunan Provincial University Key Laboratory of QSAR/QSPR; China
| | - Chenzhong Cao
- School of Chemistry and Chemical Engineering; Hunan University of Science and Technology; Xiangtan 411201 China
- Key Laboratory of Theoretical Chemistry and Molecular Simulation of Ministry of Education; Hunan University of Science and Technology; China
- Hunan Provincial University Key Laboratory of QSAR/QSPR; China
| | - Hua Yuan
- School of Chemistry and Chemical Engineering; Hunan University of Science and Technology; Xiangtan 411201 China
- Key Laboratory of Theoretical Chemistry and Molecular Simulation of Ministry of Education; Hunan University of Science and Technology; China
- Hunan Provincial University Key Laboratory of QSAR/QSPR; China
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Abstract
Computer-aided drug design (CADD) methodologies have made great advances and contributed significantly to the discovery and/or optimization of many clinically used drugs in recent years. CADD tools have likewise been applied to the discovery of inhibitors of HIV-1 integrase, a difficult and worthwhile target for the development of efficient anti-HIV drugs. This article reviews the application of CADD tools, including pharmacophore search, quantitative structure-activity relationships, model building of integrase complexed with viral DNA and quantum-chemical studies in the discovery of HIV-1 integrase inhibitors. Different structurally diverse integrase inhibitors have been identified by, or with significant help from, various CADD tools.
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Affiliation(s)
- Chenzhong Liao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, NCI-Frederick, 376 Boyles Street, Frederick, MD 21702, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, NCI-Frederick, 376 Boyles Street, Frederick, MD 21702, USA
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Oltulu O, Yaşar MM, Eroğlu E. A QSAR study on relationship between structure of sulfonamides and their carbonic anhydrase inhibitory activity using the eigenvalue (EVA) method. Eur J Med Chem 2009; 44:3439-44. [DOI: 10.1016/j.ejmech.2009.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 01/23/2009] [Accepted: 02/07/2009] [Indexed: 01/18/2023]
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Exploring the binding of HIV-1 integrase inhibitors by comparative residue interaction analysis (CoRIA). J Mol Model 2008; 15:233-45. [DOI: 10.1007/s00894-008-0399-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 09/06/2008] [Indexed: 11/26/2022]
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Xiong XQ, Zhao DM, Bu PF, Liu Y, Ren JH, Wang J, Cheng MS. CoMFA, CoMSIA and eigenvalue analysis on dibenzodioxepinone and dibenzodioxocinone derivatives as cholesteryl ester transfer protein inhibitors. Molecules 2008; 13:1822-39. [PMID: 18794787 PMCID: PMC6245342 DOI: 10.3390/molecules13081822] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 08/07/2008] [Accepted: 08/07/2008] [Indexed: 11/29/2022] Open
Abstract
CoMFA, CoMSIA and eigenvalue analysis (EVA) were performed to study the structural features of 61 diverse dibenzodioxepinone and dibenzodioxocinone analogues to probe cholesteryl ester transfer protein (CETP) inhibitory activity. Three methods yielded statistically significant models upon assessment of cross-validation, bootstrapping, and progressive scrambling. This was further validated by an external set of 13 derivatives. Our results demonstrate that three models have a good interpolation as well as extrapolation. The hydrophobic features were confirmed to contribute significantly to inhibitor potencies, while a pre-oriented hydrogen bond provided by the hydroxyl group at the 3-position indicated a good correlation with previous SAR, and a hydrogen bond acceptor may play a crucial role in CETP inhibition. These derived models may help us to gain a deeper understanding of the binding interaction of these lactone-based compounds and aid in the design of new potent compounds against CETP.
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Affiliation(s)
- Xu-qiong Xiong
- Key Lab of New Drugs Design and Discovery of Liaoning Province, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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Saíz-Urra L, González MP, Fall Y, Gómez G. Quantitative structure–activity relationship studies of HIV-1 integrase inhibition. 1. GETAWAY descriptors. Eur J Med Chem 2007; 42:64-70. [PMID: 17030481 DOI: 10.1016/j.ejmech.2006.08.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Revised: 08/11/2006] [Accepted: 08/14/2006] [Indexed: 11/21/2022]
Abstract
The GEometry, Topology, and Atom-Weights AssemblY (GETAWAY) approach has been applied to the study of the HIV-1 integrase inhibition of 172 compounds that belong to 11 different chemistry families. A model able to describe more than 68.5% of the variance in the experimental activity was developed with the use of the mentioned approach. In contrast, none of the five different approaches, including the use of Randić Molecular Profiles, Geometrical, RDF, 3D-MORSE and WHIM descriptors was able to explain more than 62.4% of the variance in the mentioned property with the same number of variables in the equation. Finally, after extracting five compounds considered by us as outliers the model was able to describe more than 72.5% of the variance in the experimental activity.
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Affiliation(s)
- Liane Saíz-Urra
- Chemical Bioactive Center, Central University of Las Villas, Santa Clara, Villa Clara, CP 54830, Cuba
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Zhang H, Venkatesha S, Minahan R, Sherman D, Oweis Y, Natarajan A, Thakor NV. Intraoperative neurological monitoring. ACTA ACUST UNITED AC 2006; 25:39-45. [PMID: 16898657 DOI: 10.1109/memb.2006.1657786] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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De-Xin K, Tao J, Hua-Shi G. Potential of Eigen Value Method to the Study on Structure-antioxidant Activity Relationship. CHINESE J CHEM 2005. [DOI: 10.1002/cjoc.200590816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Takane SY, Mitchell JBO. A structure-odour relationship study using EVA descriptors and hierarchical clustering. Org Biomol Chem 2004; 2:3250-5. [PMID: 15534702 DOI: 10.1039/b409802a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structure-odour relationship analyses using hierarchical clustering were carried out on a diverse dataset of 47 molecules. These molecules were divided into seven odour categories: ambergris, bitter almond, camphoraceous, rose, jasmine, muguet, and musk. The alignment-independent descriptor EVA (EigenVAlue) was used as the molecular descriptor. The results were compared with those of another kind of descriptor, the UNITY 2D fingerprint. The dendrograms obtained with these descriptors were compared with the seven odour categories using the adjusted Rand index. The dendrograms produced by EVA consistently outperformed those from UNITY 2D in reproducing the experimental odour classifications of these 47 molecules.
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Affiliation(s)
- Shin-ya Takane
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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Castro E, Torrens F, Toropov A, Nesterov I, Nabiev O. QSAR Modeling ANTI-HIV-1 Activities by Optimization of Correlation Weights of Local Graph Invariants. MOLECULAR SIMULATION 2004. [DOI: 10.1080/08927020412331272449] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Makhija MT, Kasliwal RT, Kulkarni VM, Neamati N. De novo design and synthesis of HIV-1 integrase inhibitors. Bioorg Med Chem 2004; 12:2317-33. [PMID: 15080929 DOI: 10.1016/j.bmc.2004.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Revised: 02/05/2004] [Accepted: 02/05/2004] [Indexed: 10/26/2022]
Abstract
Existing AIDS therapies are out of reach for most HIV-infected people in developing countries and, where available, they are limited by their toxicity and their cost. New anti-HIV agents are needed urgently to combat emerging viral resistance and reduce the side effects associated with currently available drugs. Toward this end, LeapFrog, a de novo drug design program was used to design novel, potent, and selective inhibitors of HIV-1 integrase. The designed compounds were synthesized and tested for in vitro inhibition of HIV-1 integrase. Out of the 25 compounds that were designed, and synthesized, four molecules (compounds 23, 26, 43, and 59) showed moderate to low inhibition of HIV-1 integrase for 3'-processing and 3'-strand transfer activities. Nonetheless, these compounds possess structural features not seen in known HIV-1 integrase inhibitors and thus can serve as excellent leads for further optimization of anti-HIV-1 integrase activity.
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Affiliation(s)
- Mahindra T Makhija
- Pharmaceutical Division, Department of Chemical Technology, University of Mumbai, Matunga, Mumbai 400019, India.
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Liao C, Xie A, Shi L, Zhou J, Lu X. Eigenvalue Analysis of Peroxisome Proliferator-Activated Receptor γ Agonists. ACTA ACUST UNITED AC 2003; 44:230-8. [PMID: 14741032 DOI: 10.1021/ci034109c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eigenvalue analysis (EVA) was conducted on a series of potent agonists of peroxisome proliferator-activated receptor gamma (PPARgamma). Predictive EVA quantitative structure-activity relationship (QSAR) models were established using the SYBYL package, which had conventional r2 and cross-validated coefficient (q2) values up to 0.920 and 0.587 for the AM1 method and 0.863 and 0.586 for the PM3 method, respectively. These models were validated by a test set containing 18 compounds. The capability to predict by these two models for PPARgamma agonists, with the best predictive r2pred value of 0.614 for AM1 and 0.822 for PM3 methods, set a successful example for applying a similar approach in building QSAR models for PPARalpha and -delta that could potentially offer a new opportunity in the design of novel PPAR modulators.
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Affiliation(s)
- Chenzhong Liao
- Chipscreen Biosciences, Ltd, Research Institute of Tsinghua University, Suite C301, PO Box 28, Shenzhen, Guangdong 518057, China
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Makhija MT, Kulkarni VM. Molecular electrostatic potentials as input for the alignment of HIV-1 integrase inhibitors in 3D QSAR. J Comput Aided Mol Des 2001; 15:961-78. [PMID: 11989625 DOI: 10.1023/a:1014888730876] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Comparative molecular similarity indices analysis (CoMSIA), a three-dimensional quantitative structure activity relationship (3D QSAR) paradigm, was used to examine the correlations between the calculated physicochemical properties and the in vitro activities (3'-processing and 3'-strand transfer inhibition) of a series of human immunodeficiency virus type 1 (HIV-1) integrase inhibitors. The training set consisted of 34 molecules from five structurally diverse classes: salicylpyrazolinones, dioxepinones, coumarins, quinones, and benzoic hydrazides. The data set was aligned using extrema of molecular electrostatic potentials (MEPs). The predictive ability of the resultant model was evaluated using a test set comprised of 7 molecules belonging to a different structural class of thiazepinediones. A CoMSIA model using an MEP-based alignment showed considerable internal as well external predictive ability (r2(cv) = 0.821, r2(pred) = 0.608 for 3'-processing; and r2(cv) = 0.759, r2(pred.) = 0.660 for 3'-strand transfer).
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Affiliation(s)
- M T Makhija
- Pharmaceutical Division, Department of Chemical Technology, University of Mumbai, Matunga, India
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