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Sumalatha S, Venkataramaiah C, Naga Raju C. Design, synthesis, in vitro and in silico bioactivity profiles of new urea/thiourea derivatives of 2-pyridyl piperazine as potent antioxidant and antimicrobial agents: chemo-bio-computational approach. J Biomol Struct Dyn 2022:1-12. [PMID: 35532099 DOI: 10.1080/07391102.2022.2072952] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Synthesis of a series of new urea and thiourea derivatives of 2-pyridyl piperazine was accomplished by reacting various isocyanates and isothiocyanates in the presence of triethylamine (TEA) at 50 °C. All the title compounds were obtained in high yields and their structures were characterized by IR, 1H, 13C NMR, Mass spectral, and Elemental analysis. The synthesized compounds were screened for in vitro and in silico antioxidant and antimicrobial activities. All the title compounds exhibited potent antioxidant and antimicrobial activities. Out of all, 2c and 2f against DPPH, H2O2 and Nitro oxide have exhibited significant activity and the levels of activity were higher than the reference compounds, ascorbic acid and BHT. Whereas 2a, 2c, 2f and 2j have shown prominent activity in terms of zone of inhibition against all the microbial strains tested than the standards such as levofloxacin and nystatin. In addition in silico studies also conveyed the same that is 2a, 2c, 2f and 2j have displayed the highest binding energies against peroxiredoxins and DNA gyrase protein than the standards akin to the rest of the compounds. In overall, 2c and 2f have exhibited most promising antioxidant and antimicrobial activity than the rest of the title compounds in vitro and in silico. Hence, 2c and 2f will stand as a lead and promising antioxidant and antimicrobial drug candidates in future.
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Affiliation(s)
- S Sumalatha
- Department of Chemistry, Sri Venkateswara University, Tirupati, India
| | - Ch Venkataramaiah
- Department of Zoology, Sri Venkateswara University, Tirupati, India.,Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - C Naga Raju
- Department of Chemistry, Sri Venkateswara University, Tirupati, India
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2
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Synthesis, spectral characterization, docking studies and biological activity of urea, thiourea, sulfonamide and carbamate derivatives of imatinib intermediate. Mol Divers 2018; 23:723-738. [DOI: 10.1007/s11030-018-9906-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
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3
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Vedavathi P, Sudhamani H, Raju CN. Synthesis and antimicrobial activity of new urea and thiourea derivatives of (2′-(1H-tetrazol-5-yl)biphenyl-4-yl)methanamine. RESEARCH ON CHEMICAL INTERMEDIATES 2016. [DOI: 10.1007/s11164-016-2823-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Montgomery T, Rawal VH. Palladium-Catalyzed Modular Synthesis of Substituted Piperazines and Related Nitrogen Heterocycles. Org Lett 2016; 18:740-3. [PMID: 26824482 PMCID: PMC4991562 DOI: 10.1021/acs.orglett.5b03708] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Indexed: 11/30/2022]
Abstract
We report here a novel method for the modular synthesis of highly substituted piperazines and related bis-nitrogen heterocycles via a palladium-catalyzed cyclization reaction. The process couples two of the carbons of a propargyl unit with various diamine components to provide nitrogen heterocycles in generally good to excellent yields and high regio- and stereochemical control.
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Affiliation(s)
- Thomas
D. Montgomery
- Department
of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Viresh H. Rawal
- Department
of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
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5
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Mohandas T, Krishnan KG, Balamurugan S, Harrison WTA, Thanikachalam V, Sakthivel P. Crystal structure of ( E)-4-(acetoxyimino)- N-allyl-3-isopropyl-2,6-diphenylpiperidine-1-carbothioamide. Acta Crystallogr E Crystallogr Commun 2015; 71:o542-3. [PMID: 26396787 PMCID: PMC4571387 DOI: 10.1107/s2056989015012499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 06/29/2015] [Indexed: 11/12/2022]
Abstract
The title compound, C26H31N3O2S, crystallizes with two molecules (A and B) in the asymmetric unit. In each case, the piperidine ring exists in a twist-boat conformation. The dihedral angle between the phenyl rings is 46.16 (12)° in molecule A and 44.95 (12)° in molecule B. In both molecules, the allyl side chain is disordered over two orientations in a 0.649 (9):0.351 (9) ratio for molecule A and 0.826 (10):0.174 (10) ratio for molecule B. In the crystal, neither molecule forms a hydrogen bond from its N—H group, presumably due to steric hindrance. A+A and B+B inversion dimers are formed, linked by pairs of weak C—H⋯O hydrogen bonds enclosing R22(22) ring motifs.
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Inhibition of protein glycation by urea and thiourea derivatives of glycine/proline conjugated benzisoxazole analogue – Synthesis and structure–activity studies. Eur J Med Chem 2013; 60:325-32. [DOI: 10.1016/j.ejmech.2012.12.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 12/08/2012] [Accepted: 12/11/2012] [Indexed: 11/23/2022]
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7
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Takkis K, Sild S. QSAR Modeling of HIV-1 Protease Inhibition on Six- and Seven-membered Cyclic Ureas. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200860006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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8
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Synthesis, characterization and in vitro antibacterial activity of thiourea and urea derivatives of steroids. Eur J Med Chem 2008; 43:2272-7. [DOI: 10.1016/j.ejmech.2007.12.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 12/08/2007] [Accepted: 12/11/2007] [Indexed: 11/21/2022]
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9
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Yoshida T, Yamagishi K, Chuman H. QSAR Study of Cyclic Urea Type HIV-1 PR Inhibitors Using Ab Initio
MO Calculation of Their Complex Structures with HIV-1 PR. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/qsar.200730108] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Natera J, Otero L, Sereno L, Fungo F, Wang NS, Tsai YM, Hwu TY, Wong KT. A Novel Electrochromic Polymer Synthesized through Electropolymerization of a New Donor−Acceptor Bipolar System. Macromolecules 2007. [DOI: 10.1021/ma070055m] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Horvath D, Bonachera F, Solov'ev V, Gaudin C, Varnek A. Stochastic versus Stepwise Strategies for Quantitative Structure−Activity Relationship GenerationHow Much Effort May the Mining for Successful QSAR Models Take? J Chem Inf Model 2007; 47:927-39. [PMID: 17480052 DOI: 10.1021/ci600476r] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Descriptor selection in QSAR typically relies on a set of upfront working hypotheses in order to boil down the initial descriptor set to a tractable size. Stepwise regression, computationally cheap and therefore widely used in spite of its potential caveats, is most aggressive in reducing the effectively explored problem space by adopting a greedy variable pick strategy. This work explores an antipodal approach, incarnated by an original Genetic Algorithm (GA)-based Stochastic QSAR Sampler (SQS) that favors unbiased model search over computational cost. Independent of a priori descriptor filtering and, most important, not limited to linear models only, it was benchmarked against the ISIDA Stepwise Regression (SR) tool. SQS was run under various premises, varying the training/validation set splitting scheme, the nonlinearity policy, and the used descriptors. With the considered three anti-HIV compound sets, repeated SQS runs generate sometimes poorly overlapping but nevertheless equally well validating model sets. Enabling SQS to apply nonlinear descriptor transformations increases the problem space: nevertheless, nonlinear models tend to be more robust validators. Model validation benchmarking showed SQS to match the performance of SR or outperform it in cases when the upfront simplifications of SR "backfire", even though the robust SR got trapped in local minima only once in six cases. Consensus models from large SQS model sets validate well--but not outstandingly better than SR consensus equations. SQS is thus a robust QSAR building tool according to standard validation tests against external sets of compounds (of same families as used for training), but many of its benefits/drawbacks may yet not be revealed by such tests. SQS results are a challenge to the traditional way to interpret and exploit QSAR: how to deal with thousands of well validating models, nonetheless providing potentially diverging applicability ranges and predicted values for external compounds. SR does not impose such burden on the user, but is "betting" on a single equation or a narrow consensus model to behave properly in virtual screening a sound strategy? By posing these questions, this article will hopefully act as an incentive for the long-haul studies needed to get them answered.
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Affiliation(s)
- Dragos Horvath
- UGSF-UMR 8576 CNRS/USTL, Université de Lille 1, Bât C9., 59650 Villeneuve d'Ascq, France.
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Vilar S, Villaverde MC, Sussman F. Inhibitor docking screened by the modified SAFE_p scoring function: Application to cyclic urea HIV-1 PR inhibitors. J Comput Chem 2007; 28:2216-25. [PMID: 17450567 DOI: 10.1002/jcc.20741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Our laboratory has in the past developed a method for the prediction of ligand binding free energies to proteins, referred to as SAFE_p (Solvent free energy predictor). Previously, we have applied this protocol for the prediction of the binding free energy of peptidic and cyclic urea HIV-1 PR inhibitors, whose X-ray structures bound to enzyme are known. In this work, we present the first account of a docking simulation, where the ligand conformations were screened and inhibitor ranking was predicted on the basis of a modified SAFE_p approach, for a set of cyclic urea-HIV-1 PR complexes whose structures are not known. We show that the optimal dielectric constant for docking is rather high, in line with the values needed to reproduce some protein residue properties, like pKa's. Our protocol is able to reproduce most of the observed binding ranking, even in the case that the components of the equation are not fitted to experimental data. Partition of the binding free energy into pocket and residue contributions sheds light into the importance of the inhibitor's fragments and on the prediction of "hot spots" for resistance mutations.
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Affiliation(s)
- Santiago Vilar
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, 15782-Santiago de Compostela, Spain
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Vilar S, Santana L, Uriarte E. Probabilistic Neural Network Model for the In Silico Evaluation of Anti-HIV Activity and Mechanism of Action. J Med Chem 2006; 49:1118-24. [PMID: 16451076 DOI: 10.1021/jm050932j] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A theoretical model has been developed that discriminates between active and nonactive drugs against HIV-1 with four different mechanisms of action for the active drugs. The model was built up using a probabilistic neural network (PNN) algorithm and a database of 2720 compounds. The model showed an overall accuracy of 97.34% in the training series, 85.12% in the selection series, and 84.78% in an external prediction series. The model not only correctly classified a very heterogeneous series of organic compounds but also discriminated between very similar active/nonactive chemicals that belong to the same family of compounds. More specifically, the model recognized 96.02% of nonactive compounds, 94.24% of active compounds that inhibited reverse transcriptase, 97.24% of protease inhibitors, 97.14% of virus uncoating inhibitors, and 90.32% of integrase inhibitors. The results indicate that this approach may represent a powerful tool for modeling large databases in QSAR with applications in medicinal chemistry.
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Affiliation(s)
- Santiago Vilar
- Faculty of Pharmacy, Department of Organic Chemistry, University of Santiago de Compostela, Santiago de Compostela 15782, Spain.
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14
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Frecer V, Burello E, Miertus S. Combinatorial design of nonsymmetrical cyclic urea inhibitors of aspartic protease of HIV-1. Bioorg Med Chem 2005; 13:5492-501. [PMID: 16054372 DOI: 10.1016/j.bmc.2005.06.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aspartic protease (PR) of the human immunodeficiency virus type 1 (HIV-1) is an important target for the design of specific antiviral agents dedicated to treatment of HIV-1 infection. We have employed computer-assisted combinatorial chemistry methods to design a small focused virtual library of nonsymmetrically substituted cyclic urea inhibitors of the PR. Nonsymmetrical compounds with decreased peptidic character were namely found to inhibit the PR with comparable inhibition potencies as their C2-pseudosymmetric counterparts and to possess superior pharmacokinetic properties. To generate the virtual library of fully nonsymmetrical cyclic urea analogs, diverse reagents were selected from databases of available chemicals with characteristics similar to those of the building blocks of known potent PR inhibitors. The X-ray structure of the protease-inhibitor complex PR-XV-638 was used as the receptor model in the structure-based focusing and in silico screening of the virtual library. A target-specific LUDI-type scoring function, parameterized for a QSAR training set of known cyclic urea inhibitors and validated on a set of compounds not included into the training set, was used to predict the inhibition constants (Ki) of the generated analogs toward the HIV-1 PR. The fragments most frequently occurring in the analogs with the highest predicted inhibition potencies (Ki*<10 pM) were then selected to constitute a highly focused library subset containing novel nonsymmetrical cyclic ureas with predicted Ki*s 1 order of magnitude lower than the most potent known cyclic urea inhibitors. ADME properties calculated for the most promising analogs suggested that the cyclic ureas are endowed with a wide range of favorable pharmacokinetic properties, which may favor the discovery of a potent orally administrable antiviral drug.
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Affiliation(s)
- Vladimír Frecer
- International Centre for Science and High Technology, UNIDO, AREA Science Park, Padriciano 99, I-34012 Trieste, Italy
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15
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Parish CA, Yarger M, Sinclair K, Dure M, Goldberg A. Comparing the conformational behavior of a series of diastereomeric cyclic urea HIV-1 inhibitors using the low mode:monte carlo conformational search method. J Med Chem 2004; 47:4838-50. [PMID: 15369387 DOI: 10.1021/jm049716l] [Citation(s) in RCA: 8] [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
The conformational flexibility of a series of diastereomeric cyclic urea HIV-1 protease inhibitors has been examined using the Low Mode:Monte Carlo conformational search method. Force fields were validated by a comparison of the energetic ordering of the minimum energy structures on the AMBER/GBSA(water), OPLSAA/GBSA(water) and HF/6-311G/SCRF(water) surfaces. The energetic ordering of the minima on the OPLSAA /GBSA(water) surface was in better agreement with the quantum calculations than the ordering on the AMBER/GBSA(water) surface. An ensemble of low energy structures was generated using OPLSAA/GBSA(water) and used to compare the molecular shape and flexibility of each diastereomer to the experimentally determined binding affinities and crystal structures of closely related systems. The results indicate that diastereomeric solution-phase energetic stability, conformational rigidity and ability to adopt a chair conformation correlate strongly with experimental binding affinities. Rigid body docking suggests that all of the diastereomers adopt solution-phase conformations suitable for alignment with the HIV-1 protease; however, these results indicate that the binding affinities are dependent upon subtle differences in the P1/P1' and P2/P2' substituent orientations.
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Affiliation(s)
- Carol A Parish
- Department of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, USA.
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16
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Solov'ev VP, Varnek A. Anti-HIV activity of HEPT, TIBO, and cyclic urea derivatives: structure-property studies, focused combinatorial library generation, and hits selection using substructural molecular fragments method. ACTA ACUST UNITED AC 2004; 43:1703-19. [PMID: 14502505 DOI: 10.1021/ci020388c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Substructural molecular fragments (SMF) method [Solov'ev, V. P.; Varnek, A.; Wipff, G. J. Chem. Inf. Comput. Sci. 2000, 40, 847-858] was applied to assess anti-HIV activity for large data sets for three families of compounds: 1-[2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) derivatives, tetrahydroimidazobenzodiazepinone (TIBO) derivatives, and cyclic urea (CU) derivatives. The SMF method uses 49 types of topological descriptors (atom/bond sequences and "augmented atoms") which, being coupled with 3 linear and nonlinear fitting equations, allows the user to generate up to 147 structure-property models. For each family of compounds, the modeling was performed on several training sets followed by the validation calculations where three best fit models were applied. Calculated activities well reproduce available experimental data. On the basis of the "optimal" molecular fragments, the focused combinatorial library containing 252 virtual HEPT derivatives has been generated. Its filtering led to several hits potentially possessing anti-HIV activity.
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Affiliation(s)
- V P Solov'ev
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, 142432, Chernogolovka, Moscow Region, Russia
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Garg R, Gupta SP, Gao H, Babu MS, Debnath AK, Hansch C. Comparative Quantitative Structureminus signActivity Relationship Studies on Anti-HIV Drugs. Chem Rev 1999; 99:3525-3602. [PMID: 11849030 DOI: 10.1021/cr9703358] [Citation(s) in RCA: 204] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rajni Garg
- Department of Chemistry, Pomona College, Claremont, California 91711, Departments of Chemistry and Pharmacy, Birla Institute of Technology and Science, Pilani 333031, India, Pharmacia & Upjohn, 301 Henrietta Street, Kalamazoo, Michigan 49007, and Biochemical Virology Laboratory, Lindsley F. Kimball Research Institute of The New York Blood Center, 310 E. 67th Street, New York, New York 10021
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18
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Hilgeroth A, Wiese M, Billich A. Synthesis and biological evaluation of the first N-alkyl cage dimeric 4-aryl-1,4-dihydropyridines as novel nonpeptidic HIV-1 protease inhibitors. J Med Chem 1999; 42:4729-32. [PMID: 10579836 DOI: 10.1021/jm991115k] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A first series of novel NH and N-alkyl-substituted cage dimeric 4-aryl-1,4-dihydropyridines 3a-f has been synthesized and evaluated as HIV-1 protease inhibitors in in vitro assays. While the NH and N-methyl derivatives 3a,b,e,f were almost inactive with IC(50) values of about 200 microM, the N-Benzyl compounds exhibited stronger activity with an IC(50) value of 16.2 microM for the presently best compound 3c. The type of HIV-1 protease inhibition of these novel inhibitors was characterized as competitive. With the increase of observed activity from NH and N-methyl derivatives to N-benzyl compounds, respectively, the binding mode may correspond to that of cyclic and azacyclic ureas showing hydrophobic interactions of the four aromatic residues to the S1/S1' and S2/S2' regions of HIV-1 protease.
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Affiliation(s)
- A Hilgeroth
- Department of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle, Germany
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19
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Abstract
We explore the question of what are the best ligands for macromolecular targets. A survey of experimental data on a large number of the strongest-binding ligands indicates that the free energy of binding increases with the number of nonhydrogen atoms with an initial slope of approximately -1.5 kcal/mol (1 cal = 4.18 J) per atom. For ligands that contain more than 15 nonhydrogen atoms, the free energy of binding increases very little with relative molecular mass. This nonlinearity is largely ascribed to nonthermodynamic factors. An analysis of the dominant interactions suggests that van der Waals interactions and hydrophobic effects provide a reasonable basis for understanding binding affinities across the entire set of ligands. Interesting outliers that bind unusually strongly on a per atom basis include metal ions, covalently attached ligands, and a few well known complexes such as biotin-avidin.
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Affiliation(s)
- I D Kuntz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143-0446, USA.
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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.
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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.
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21
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De Lucca GV, Liang J, De Lucca I. Stereospecific synthesis, structure-activity relationship, and oral bioavailability of tetrahydropyrimidin-2-one HIV protease inhibitors. J Med Chem 1999; 42:135-52. [PMID: 9888839 DOI: 10.1021/jm9803626] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of tetrahydropyrimidinones as an alternate scaffold for designing HIVPR inhibitors has advantages, over the previously disclosed hexahydro-1,3-diazepin-2-ones, of being more unsymmetrical (different P1/P1'), less crystalline, more soluble, and more lipophilic (mono-ol vs diol). They show a better translation of Ki to IC90 for the more polar P2 groups that in general give the more potent enzyme inhibitors. Structure-activity relationship (SAR) studies of the tetrahydropyrimidinones showed that the phenylethyl P1' substituent, the hydroxyl group, and the urea carbonyl are all critical for good activity. However, there was significant flexibility in the possible P2/P2' substituents that could be used. Many analogues that contained identical or different P2/P2' substituents, or only one P2 substituent, were found to have excellent enzyme potency and several had excellent antiviral potency. Several of these compounds were examined for oral bioavailability in the rat or the dog at 10 mg/kg. However, the oral bioavailability of the tetrahydropyrimidinones was, in general, less than the corresponding hexahydro-1,3-diazepin-2-ones. Unfortunately, when all factors are considered, including potency, protein binding, solubility, bioavailability, and resistance profile, the tetrahydropyrimidinones did not offer any advantage over the previously disclosed hexahydro-1,3-diazepin-2-ones series.
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Affiliation(s)
- G V De Lucca
- DuPont Pharmaceuticals Company, Wilmington, Delaware 19880-0500, USA.
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22
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De Lucca GV, Jadhav PK, Waltermire RE, Aungst BJ, Erickson-Viitanen S, Lam PY. De novo design and discovery of cyclic HIV protease inhibitors capable of displacing the active-site structural water molecule. PHARMACEUTICAL BIOTECHNOLOGY 1998; 11:257-84. [PMID: 9760684 DOI: 10.1007/0-306-47384-4_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- G V De Lucca
- DuPont Merck Pharmaceutical Company, Wilmington, Delaware 19880-0500, USA
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23
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Debnath AK. Comparative molecular field analysis (CoMFA) of a series of symmetrical bis-benzamide cyclic urea derivatives as HIV-1 protease inhibitors. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 1998; 38:761-7. [PMID: 9691478 DOI: 10.1021/ci980014c] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A 3D-QSAR study using CoMFA methodology was conducted on a series of 29 symmetrical bis-benzamide cyclic urea derivatives having anti-HIV-1-protease activities. Active site minimization of the ligands was used to exclude conformations which are not sterically accessible within the active site. A significant cross validated correlation coefficient q2 (0.724) was obtained indicating the predictive potential of the model for untested compounds of this class. A significant non-cross-validated correlation coefficient (r2) of 0.971 with a low standard error estimate (S) of 0.119 was obtained indicating that the model reliably predicted the ant-protease activities of poorly to highly active compounds. The model was used to predict the anti-protease activities of eight test-set compounds, and the predicted values were in good agreement with the experimental values. The CoMFA coefficient contour plots identified several key features which explain the wide range of activities. The already reported 2D-QSAR along with the CoMFA model presented here may help in designing effective HIV-1 protease inhibitors.
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Affiliation(s)
- A K Debnath
- Biochemical Virology Laboratory, Lindsley F. Kimball Research Institute, New York Blood Center, New York 10021, USA
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De Lucca GV, Kim UT, Liang J, Cordova B, Klabe RM, Garber S, Bacheler LT, Lam GN, Wright MR, Logue KA, Erickson-Viitanen S, Ko SS, Trainor GL. Nonsymmetric P2/P2' cyclic urea HIV protease inhibitors. Structure-activity relationship, bioavailability, and resistance profile of monoindazole-substituted P2 analogues. J Med Chem 1998; 41:2411-23. [PMID: 9632373 DOI: 10.1021/jm980103g] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Using the structural information gathered from the X-ray structures of various cyclic urea/HIVPR complexes, we designed and synthesized many nonsymmetrical P2/P2'-substituted cyclic urea analogues. Our efforts concentrated on using an indazole as one of the P2 substituents since this group imparted enzyme (Ki) potency as well as translation into excellent antiviral (IC90) potency. The second P2 substituent was used to adjust the physical and chemical properties in order to maximize oral bioavailability. Using this approach several very potent (IC90 11 nM) and orally bioavailable (F% 93-100%) compounds were discovered (21, 22). However, the resistance profiles of these compounds were inadequate, especially against the double (I84V/V82F) and ritonavir-selected mutant viruses. Further modification of the second P2 substituent in order to increase H-bonding interactions with the backbone atoms of residues Asp 29, Asp 30, and Gly 48 led to analogues with much better resistance profiles. However, these larger analogues were incompatible with the apparent molecular weight requirements for good oral bioavailability of the cyclic urea class of HIVPR inhibitors (MW < 610).
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Affiliation(s)
- G V De Lucca
- Dupont Merck Pharmaceutical Company, Experimental Station, P.O. Box 80500, Wilmington, Delaware 19880-0500, USA.
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Wilkerson WW, Dax S, Cheatham WW. Nonsymmetrically substituted cyclic urea HIV protease inhibitors. J Med Chem 1997; 40:4079-88. [PMID: 9406598 DOI: 10.1021/jm970288b] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A series of nonsymmetrically substituted cyclic ureacarboxamides was synthesized and evaluated for antiviral activity as a function of the inhibition of HIV-protease. Selected protease inhibitors were also evaluated for oral bioavailability. The synthesis, pharmacology, quantitative structure-activity relationship (QSAR), and pharmacokinetics for the series will be discussed.
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Affiliation(s)
- W W Wilkerson
- DuPont Merck Pharmaceutical Company, Experimental Station, Wilmington, Delaware 19880-0500, USA
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Eyermann CJ, Jadhav P, Nicholas Hodge C, Chang CH, Rodgers JD, Y.S.L P. The role of computer-aided and structure-based design techniques in the discovery and optimization of cyclic urea inhibitors of hiv protease. ADVANCES IN AMINO ACID MIMETICS AND PEPTIDOMIMETICS 1997. [DOI: 10.1016/s1874-5113(97)80003-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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