1
|
Gouhar SA, Elshahid ZA. Molecular docking and simulation studies of synthetic protease inhibitors against COVID-19: a computational study. J Biomol Struct Dyn 2022; 40:13976-13996. [PMID: 34738871 DOI: 10.1080/07391102.2021.1997822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
COVID-19 is the most recent threat to global health. Many people preferred treatment in case of infection instead of vaccination. The inhibition of viral replication is a good strategy for the treatment of COVID-19 infection. 3CLpro and PLpro are two important viral proteases responsible for proteolysis, infection, and replication of the virus. Therefore, targeting of these two enzymes is an attractive way to deal with COVID-19. The aim of this study was to screen some synthetic protease inhibitors to determine an appropriate hit molecule against COVID-19 using molecular docking and molecular dynamic simulations. The strategy depends on docking existing synthetic compounds mostly HIV protease inhibitors against two COVID-19 proteases to identify promising drugs for the treatment of COVID-19. We used protein data bank to obtain the X-ray crystal structure of the most important COVID-19 proteases 3CL pro (PDB ID: 6M2N) and PL pro (PDB ID: 6WX4). In this conceptual context, an attempt has been made to suggest an in silico computational relationship between 50 synthetic protease inhibitors and COVID-19 proteases. Out of 50 screened compounds, the best docking scores were found for these five protease inhibitors BDBM7021, BDBM698, BDBM694, BDBM93239, BDBM700. A 100-ns MD simulation was carried out to assess the stability of COVID-19 proteases and inhibitors, revealing an average RMSD value of 0.7 and favorable binding free energy (MM-GBSA) for all complexes confirming their potency as powerful binders in the COVID-19 proteases' binding pocket. Furthermore, the current results must be confirmed using in-vitro and in-vivo antiviral methods.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shaimaa A Gouhar
- Medical Biochemistry Department, Medical Research Division, National Research Centre, Cairo, Egypt
| | - Zeinab A Elshahid
- Chemistry of Natural and Microbial Products, Pharmaceutical Industry Research Division, National Research Center, Cairo, Egypt
| |
Collapse
|
2
|
Łukowska-Chojnacka E, Kowalkowska A, Napiórkowska A. Lipase-catalyzed kinetic resolution of novel antitubercular benzoxazole derivatives. Chirality 2017; 30:457-468. [DOI: 10.1002/chir.22806] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/11/2017] [Accepted: 11/22/2017] [Indexed: 01/31/2023]
Affiliation(s)
| | - Anna Kowalkowska
- Faculty of Chemistry; Warsaw University of Technology; Warsaw Poland
| | - Agnieszka Napiórkowska
- Microbiology Department; National Tuberculosis and Lung Diseases Research Institute; Warsaw Poland
| |
Collapse
|
3
|
Alberti MN, Polyhach Y, Tzirakis MD, Tödtli L, Jeschke G, Diederich F. Exploring the Strength of the H-Bond in Synthetic Models for Heme Proteins: The Importance of the N−H Acidity of the Distal Base. Chemistry 2016; 22:10194-202. [DOI: 10.1002/chem.201601505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Mariza N. Alberti
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - Manolis D. Tzirakis
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Laura Tödtli
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| |
Collapse
|
4
|
Docking and 3-D QSAR studies on the binding of tetrahydropyrimid-2-one HIV-1 protease inhibitors. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.03.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
5
|
Armitage M, Bret G, Choudary BM, Kingswood M, Loft M, Moore S, Smith S, Urquhart MWJ. Identification and Development of an Efficient Route to SB-649915. Org Process Res Dev 2012. [DOI: 10.1021/op300185s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mark Armitage
- Glaxo Group Limited, Medicines Research Centre, Gunnels
Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Guillaume Bret
- Glaxo Group Limited, Medicines Research Centre, Gunnels
Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Bernie M. Choudary
- Glaxo Group Limited, Medicines Research Centre, Gunnels
Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Mike Kingswood
- Glaxo Group Limited, Medicines Research Centre, Gunnels
Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Mike Loft
- Glaxo Group Limited, Medicines Research Centre, Gunnels
Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Steve Moore
- Glaxo Group Limited, Medicines Research Centre, Gunnels
Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Steve Smith
- Glaxo Group Limited, Medicines Research Centre, Gunnels
Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Michael W. J. Urquhart
- Glaxo Group Limited, Medicines Research Centre, Gunnels
Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| |
Collapse
|
6
|
Synthesis and in vitro antimycobacterial and isocitrate lyase inhibition properties of novel 2-methoxy-2′-hydroxybenzanilides, their thioxo analogues and benzoxazoles. Eur J Med Chem 2012; 56:108-19. [DOI: 10.1016/j.ejmech.2012.08.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 08/08/2012] [Accepted: 08/10/2012] [Indexed: 11/22/2022]
|
7
|
Synthesis and biological evaluation of oxadiazole derivatives as inhibitors of soluble guanylyl cyclase. Bioorg Med Chem 2009; 18:1288-96. [PMID: 20036129 DOI: 10.1016/j.bmc.2009.12.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 12/02/2009] [Accepted: 12/08/2009] [Indexed: 11/20/2022]
Abstract
Soluble guanylyl cyclase (sGC) is an ubiquitously expressed enzyme that generates the second messenger cGMP and hence, leads to a number of physiological responses including vasodilation, inhibition of platelet aggregation and neurotransmission. Whilst many activating and stimulating modulators of sGC were identified and studied in recent years, only two selective inhibitors are known: ODQ and NS 2028. Furthermore, a synthetic approach to these inhibitors has not been reported yet. Herein, we describe a novel and efficient synthesis of these inhibitors, as well as the preparation of three different classes of NS 2028 analogues. Biological evaluation of this library using rat aortic smooth muscle cells revealed four new compounds with good to moderate sGC inhibitory activity. Our experiments underline the major importance of the oxadiazole ring in ODQ and NS 2028 for the efficiency of this class of inhibitors.
Collapse
|
8
|
Giles R, Sullivan J, Steiner A, Looper R. Addition-Hydroamination Reactions of Propargyl Cyanamides: Rapid Access to Highly Substituted 2-Aminoimidazoles. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900160] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
9
|
Giles R, Sullivan J, Steiner A, Looper R. Addition-Hydroamination Reactions of Propargyl Cyanamides: Rapid Access to Highly Substituted 2-Aminoimidazoles. Angew Chem Int Ed Engl 2009; 48:3116-20. [DOI: 10.1002/anie.200900160] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
10
|
Lena G, Lallemand E, Gruner AC, Boeglin J, Roussel S, Schaffner AP, Aubry A, Franetich JF, Mazier D, Landau I, Briand JP, Didierjean C, Rénia L, Guichard G. 1,3,5-Triazepan-2,6-diones as Structurally Diverse and Conformationally Constrained Dipeptide Mimetics: Identification of Malaria Liver Stage Inhibitors from a Small Pilot Library. Chemistry 2006; 12:8498-512. [PMID: 16927352 DOI: 10.1002/chem.200600560] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The development of the 1,3,5-triazepane-2,6-dione system as a novel, conformationally restricted, and readily accessible class of dipeptidomimetics is reported. The synthesis of the densely functionalized 1,3,5-triazepane-2,6-dione skeleton was achieved in only four steps from a variety of simple linear dipeptide precursors. To extend the practical value of 1,3,5-triazepane-2,6-diones, a general polymer-assisted solution-phase synthesis approach amenable to library production in a multiparallel format was developed. The conformational preferences of the 1,3,5-triazepane-2,6-dione skeleton were investigated in detail by NMR spectroscopy and X-ray diffraction. The ring exhibits a characteristic folded conformation which was compared to that of related dipeptide-derived scaffolds including the more planar 2,5-diketopiperazine (DKP). Molecular and structural diversity was increased further through post-cyclization appending operations at urea nitrogens. Preliminary biological screens of a small collection of 1,3,5-triazepane-2,6-diones revealed inhibitors of the underexplored malaria liver stage and suggest strong potential for this dipeptide-derived scaffold to interfere with and to modulate biological pathways.
Collapse
Affiliation(s)
- Gersande Lena
- Immunologie et Chimie Thérapeutiques (ICT), UPR CNRS 9021, Institut de Biologie Moléculaire et Cellulaire, 15 rue Descartes, 67084 Strasbourg, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Leung LM, Gibson V, Linclau B. Improved synthesis of enantiopure pseudo-C2-symmetric 1,4-bis-epoxide building blocks from arabitol. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.tetasy.2005.05.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
12
|
Lin TH, Li HT, Tsai KC. Implementing the Fisher's discriminant ratio in a k-means clustering algorithm for feature selection and data set trimming. ACTA ACUST UNITED AC 2004; 44:76-87. [PMID: 14741013 DOI: 10.1021/ci030295a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Fisher's discriminant ratio has been used as a class separability criterion and implemented in a k-means clustering algorithm for performing simultaneous feature selection and data set trimming on a set of 221 HIV-1 protease inhibitors. The total number of molecular descriptors computed for each inhibitor is 43, and they are scaled to lie between 1 and 0 before being subjected to the feature selection process. Since the purpose is to select some of the most class sensitive descriptors, several feature evaluation indices such as the Shannon entropy, the linear regression of selected descriptors on the pKi of selected inhibitors, and a stepwise variable selection program are used to filter them. While the Shannon entropy provides the information content for each descriptor computed, more class sensitive descriptors are searched by both the linear regression and stepwise variable selection procedures. The inhibitors are divided into several different numbers of classes. They are subsequently divided into five classes due to the fact that the best feature selection result is obtained by the division. Most of the good features selected are the topological descriptors, and they are correlated well with the pKi values. The outliers or the inhibitors with less class-sensitive descriptor values computed for each selected descriptor are identified and gathered by the k-means clustering algorithm. These are the trimmed inhibitors, while the remaining ones are retained or selected. We find that 44% or 98 inhibitors can be retained when the number of good descriptors selected for clustering is three. The descriptor values of these selected inhibitors are far more class sensitive than the original ones as evidenced by substantial increasing in statistical significance when they are subjected to both the SYBYL CoMFA PLS and Cerius2 PLS regression analyses.
Collapse
Affiliation(s)
- Thy-Hou Lin
- Institute of Molecular Medicine & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC.
| | | | | |
Collapse
|
13
|
Jun JH, Dougherty JM, Jiménez MDS, Hanson PR. New strategies to symmetric and unsymmetric cyclic sulfamide analogs of DMP 323: a ‘sulfur linchpin’/RCM approach. Tetrahedron 2003. [DOI: 10.1016/j.tet.2003.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
14
|
Boydell AJ, Jeffery MJ, Bürkstümmer E, Linclau B. Short Synthesis of Enantiopure C2-Symmetric 1,2:4,5-Diepoxypentane and “Pseudo”-C2-Symmetric 3-Azido-1,2:4,5-diepoxypentane from Arabitol. J Org Chem 2003; 68:8252-5. [PMID: 14535812 DOI: 10.1021/jo034374x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
On the basis of our previously described selective protection of arabitol as its 1,2:4,5-bis-pentylidene acetal 5, we report a straightforward synthesis of the novel "pseudo"-C(2)-symmetric 3-azido-1,2:4,5-diepoxypentane building block 4 in 6 steps from arabitol. Using a similar synthetic route, an improved synthesis of the C(2)-symmetrical 1,2:4,5-bis-epoxypentane building block 1 is described, also in 6 steps from arabitol. Both enantiomers of 1 and 4 are accessible, and all reactions involved are easily amenable for large-scale synthesis.
Collapse
Affiliation(s)
- A James Boydell
- Department of Chemistry, Southampton University, Highfield, Southampton SO17 1BJ, UK
| | | | | | | |
Collapse
|
15
|
Dhar TGM, Watterson SH, Chen P, Shen Z, Gu HH, Norris D, Carlsen M, Haslow KD, Pitts WJ, Guo J, Chorba J, Fleener CA, Rouleau KA, Townsend R, Hollenbaugh D, Iwanowicz EJ. Quinolone-based IMPDH inhibitors: introduction of basic residues on ring D and SAR of the corresponding mono, di and benzofused analogues. Bioorg Med Chem Lett 2003; 13:547-51. [PMID: 12565969 DOI: 10.1016/s0960-894x(02)00945-9] [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: 10/27/2022]
Abstract
The synthesis and the structure-activity relationships (SAR) of analogues derived from the introduction of basic residues on ring D of quinolone-based inhibitors of IMPDH are described. This led to the identification of compound 27 as a potent inhibitor of IMPDH with significantly improved aqueous solubility over the lead compound 1.
Collapse
|
16
|
Lin TH, Wang GM, Hsu YH. Classification of some active HIV-1 protease inhibitors and their inactive analogues using some uncorrelated three-dimensional molecular descriptors and a fuzzy c-means algorithm. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2002; 42:1490-504. [PMID: 12444748 DOI: 10.1021/ci0203747] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A fuzzy c-means algorithm was used to classify some 3D convex hull descriptors computed for 345 active HIV-1 protease inhibitors collected from literature and 437 inactive analogues searched from the MDL/ISIS database. The number of descriptors used to represent each compound was from 4 to 8, and they were uncorrelated using the principal component analysis. These uncorrelated descriptors were then divided into two groups and classified by the fuzzy c-means algorithm. The classification produced a clear-cut switch in membership functions computed for each uncorrelated descriptor at the group boundary. Compounds with nonswitching membership functions computed were treated as outliers, and they were counted for estimating the accuracy of the classification. The averaged accuracy of classification for the active inhibitor set was about 80% which was better than that directly classified by a linear discriminant function on the original 3D convex hull descriptors. The whole classification scheme was also applied to several sets of some conventional descriptors computed for each compound, but the averaged accuracy was around 58%. Further classification using some 3D convex hull descriptors searched from comparing the distribution of these descriptors was performed on a new data set composed of 289 outliers-deducted active inhibitors and 63 outliers identified from the inactive analogues through previous classification. This final classification identified 19 inactive analogues which were similar in structural and topological features to those of some highly active inhibitors classified together with them.
Collapse
Affiliation(s)
- Thy-Hou Lin
- Department of Life Science, National Tsing Hua, University, Hsinchu, Taiwan 30043, R.O.C.
| | | | | |
Collapse
|
17
|
Di Santo R, Costi R, Artico M, Massa S, Ragno R, Marshall GR, La Colla P. Design, synthesis and QSAR studies on N-aryl heteroarylisopropanolamines, a new class of non-peptidic HIV-1 protease inhibitors. Bioorg Med Chem 2002; 10:2511-26. [PMID: 12057640 DOI: 10.1016/s0968-0896(02)00119-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A series of N-aryl heteroarylisopropanolamines in which an indole or a 3-arylpyrrole moiety was linked to an aryl group through an isopropanolamine linker, were designed and synthesized as potential anti-HIV-1-PR agents. Series was tested for their ability in blocking PR activity. As a rule, indole derivatives of class 1 exhibited more potency than pyrrole analogues of class 2 while tert-butylamide substituents increased anti-PR potency. In fact, bis tert-butylamide 1e showed the highest activity with IC(50)=25 microM. Even if not very potent, a simple class of anti-PR agents, with a facile synthetic pathway was discovered. QSAR studies on isopropanolamines 1 and 2 were performed in comparison with diarylbutanols, a new class of non peptidic anti-PR agents, recently discovered by Agouron Pharmaceuticals. QSAR and CoMFA models based on 30 diarylbutanols used as a training set were developed. The obtained models were used to investigate the binding mode of the newly synthesized derivatives 1 and 2. The results of this study suggest that N-aryl heteroarylisopropanolamines bind to the PR active site similarly to the diarylbutanols of Agouron.
Collapse
Affiliation(s)
- Roberto Di Santo
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Studi Farmaceutici, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, I-00185 Rome, Italy
| | | | | | | | | | | | | |
Collapse
|
18
|
Mérour JY, Mayer S, Guillaumet G. Regioselective Formylation of Ethyl 3,4-Dihydro-2H-1,4- benzoxazine-2-carboxylate or 2-Acetate Derivatives. HETEROCYCLES 2001. [DOI: 10.3987/com-01-9302] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
19
|
Kotamarthi B, Bonin I, Benedetti F, Miertus S. Computational design of new cyclic urea inhibitors for improved binding of HIV-1 aspartic protease. Biochem Biophys Res Commun 2000; 268:384-9. [PMID: 10679213 DOI: 10.1006/bbrc.2000.2139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report in this paper the design, by means of computational techniques, of new cyclic urea inhibitors of the HIV aspartic protease. The relationship between the complexation energies of the enzyme with known inhibitors and the experimentally determined log K(i) have been studied and used to predict inhibition constants for new inhibitors.
Collapse
Affiliation(s)
- B Kotamarthi
- International Centre for Science and High Technology, UNIDO, Trieste, Italy
| | | | | | | |
Collapse
|
20
|
Alterman M, Andersson HO, Garg N, Ahlsén G, Lövgren S, Classon B, Danielson UH, Kvarnström I, Vrang L, Unge T, Samuelsson B, Hallberg A. Design and fast synthesis of C-terminal duplicated potent C(2)-symmetric P1/P1'-modified HIV-1 protease inhibitors. J Med Chem 1999; 42:3835-44. [PMID: 10508432 DOI: 10.1021/jm9910371] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An analysis of the X-ray structure of a complex of HIV-1 protease with a linear C(2)-symmetric C-terminal duplicated inhibitor guided the selection of a series of diverse target compounds. These were synthesized with the objective to identify suitable P1/P1' substituents to provide inhibitors with improved antiviral activity. Groups with various physical properties were attached to the para-positions of the P1/P1' benzyloxy groups in the parent inhibitor. A p-bromobenzyloxy compound, prepared in only three steps from commercially available starting materials, was utilized as a common precursor in all reactions. The subsequent coupling reactions were completed within a few minutes and relied on palladium catalysis and flash heating with microwave irradiation. All of the compounds synthesized exhibited good inhibitory potency in the protease assay, with K(i) values ranging from 0.09 to 3.8 nM. A 30-fold improvement of the antiviral effect in cell culture, compared to the parent compound, was achieved with four of the inhibitors. The differences in K(i) values were not correlated to the differences in antiviral effect, efficiency against mutant virus, or reduced potency in the presence of human serum. The poorest enzyme inhibitors in fact belong to the group with the best antiviral effect. The binding features of two structurally related inhibitors, cocrystallized with HIV-1 protease, are discussed with special emphasis on the interaction at the enzyme/water phase.
Collapse
Affiliation(s)
- M Alterman
- Department of Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Debnath AK. Three-dimensional quantitative structure-activity relationship study on cyclic urea derivatives as HIV-1 protease inhibitors: application of comparative molecular field analysis. J Med Chem 1999; 42:249-59. [PMID: 9925730 DOI: 10.1021/jm980369n] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three-dimensional quantitative structure-activity relationship (3D-QSAR) models have been developed using comparative molecular field analysis (CoMFA) on a large data set (118 compounds) of diverse cyclic urea derivatives as protease inhibitors against the human immunodeficiency virus type 1 (HIV-1). X-ray crystal structures of HIV-1 protease bound with this class of inhibitors were used to derive the most probable bioactive conformations of the inhibitors. The enzyme active site was used as a constraint to limit the number of possible conformations that are sterically accessible. The test sets have been created keeping in mind structural diversity as well as the uniform simple statistical criteria (mean, standard deviation, high and low values) of the protease inhibitory activities of the molecules compared to the training sets. Multiple predictive models have been developed with the training sets (93 compounds in each set) and validated with the corresponding test sets (25 compounds in each set). All the models yielded high predictive correlation coefficients (q2 from 0.699 to 0.727), substantially high fitted correlation coefficients (r2 from 0.965 to 0.973), and reasonably low standard errors of estimates (S from 0. 239 to 0.265). The steric and electrostatic effects have approximately equal contributions, 45% and 55% (approximately), respectively, toward explaining protease inhibitory activities. This analysis yielded models with significant information on steric and electrostatic interactions clearly discerned by the respective coefficient contour plots when overlapped on the X-ray structure of the HIV-1 protease. The HINT CoMFA study revealed significant contribution of hydrophobicity toward protease inhibitory activity. The 3D visualization technique utilizing these contour plots as well as the receptor site geometry may significantly improve our understanding of the inhibitor-protease (HIV-1) interactions and help in designing compounds with improved activity.
Collapse
Affiliation(s)
- A K Debnath
- Biochemical Virology Laboratory, Lindsley F. Kimball Research Institute of The New York Blood Center, 310 East 67th Street, New York, New York 10021, USA.
| |
Collapse
|