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Yadav N, Bhardwaj G, Anjum SG, Dalela S, Siddiqui MJ, Alvi PA. Investigation of high optical gain in complex type-II InGaAs/InAs/GaAsSb nano-scale heterostructure for MIR applications. Appl Opt 2017; 56:4243-4249. [PMID: 29047845 DOI: 10.1364/ao.56.004243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This paper reports a comprehensive theoretical study of W-shaped complex type-II InGaAs/InAs/GaAsSb nano-scale heterostructure consisting of two quantum wells of InAs material using the six-band k.p theory. The entire structure has been supposed to be grown on InP substrate. In order to optimize the optical gain, the probability densities of electrons and holes were optimized in the heterostructure. Following these calculations, dispersion relations for electron and hole energies, and transverse electric and transverse magnetic polarizations dependent dipole matrix elements and momentum matrix elements were calculated and, finally, the optical gain in both polarization modes was calculated. For this optimized complex heterostructure, a very high optical gain of the order of ∼4500 cm-1 in the regime of mid-infrared wavelength ∼3.2 μm has been achieved. The results suggest that the designed nano-heterostructure may be utilized for mid-infrared region (MIR) applications such as chemical and bio-molecular sensing of molecules, for the applications of spectroscopy in the "fingerprint region" of molecular science, and for detection of atmospheric gases that respond to 3.2 μm wavelength.
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Ali A, Kiran Kumar Reddy GS, Nalam MNL, Anjum SG, Cao H, Schiffer CA, Rana TM. Structure-based design, synthesis, and structure-activity relationship studies of HIV-1 protease inhibitors incorporating phenyloxazolidinones. J Med Chem 2010; 53:7699-708. [PMID: 20958050 PMCID: PMC2996262 DOI: 10.1021/jm1008743] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of new HIV-1 protease inhibitors with the hydroxyethylamine core and different phenyloxazolidinone P2 ligands were designed and synthesized. Variation of phenyl substitutions at the P2 and P2' moieties significantly affected the binding affinity and antiviral potency of the inhibitors. In general, compounds with 2- and 4-substituted phenyloxazolidinones at P2 exhibited lower binding affinities than 3-substituted analogues. Crystal structure analyses of ligand-enzyme complexes revealed different binding modes for 2- and 3-substituted P2 moieties in the protease S2 binding pocket, which may explain their different binding affinities. Several compounds with 3-substituted P2 moieties demonstrated picomolar binding affinity and low nanomolar antiviral potency against patient-derived viruses from HIV-1 clades A, B, and C, and most retained potency against drug-resistant viruses. Further optimization of these compounds using structure-based design may lead to the development of novel protease inhibitors with improved activity against drug-resistant strains of HIV-1.
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Affiliation(s)
- Akbar Ali
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - G. S. Kiran Kumar Reddy
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Saima Ghafoor Anjum
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Hong Cao
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Tariq M. Rana
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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Altman MD, Ali A, Reddy GSKK, Nalam MNL, Anjum SG, Cao H, Chellappan S, Kairys V, Fernandes MX, Gilson MK, Schiffer CA, Rana TM, Tidor B. HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J Am Chem Soc 2008; 130:6099-113. [PMID: 18412349 PMCID: PMC3465729 DOI: 10.1021/ja076558p] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The acquisition of drug-resistant mutations by infectious pathogens remains a pressing health concern, and the development of strategies to combat this threat is a priority. Here we have applied a general strategy, inverse design using the substrate envelope, to develop inhibitors of HIV-1 protease. Structure-based computation was used to design inhibitors predicted to stay within a consensus substrate volume in the binding site. Two rounds of design, synthesis, experimental testing, and structural analysis were carried out, resulting in a total of 51 compounds. Improvements in design methodology led to a roughly 1000-fold affinity enhancement to a wild-type protease for the best binders, from a Ki of 30-50 nM in round one to below 100 pM in round two. Crystal structures of a subset of complexes revealed a binding mode similar to each design that respected the substrate envelope in nearly all cases. All four best binders from round one exhibited broad specificity against a clinically relevant panel of drug-resistant HIV-1 protease variants, losing no more than 6-13-fold affinity relative to wild type. Testing a subset of second-round compounds against the panel of resistant variants revealed three classes of inhibitors: robust binders (maximum affinity loss of 14-16-fold), moderate binders (35-80-fold), and susceptible binders (greater than 100-fold). Although for especially high-affinity inhibitors additional factors may also be important, overall, these results suggest that designing inhibitors using the substrate envelope may be a useful strategy in the development of therapeutics with low susceptibility to resistance.
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Affiliation(s)
- Michael D. Altman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Akbar Ali
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - G. S. Kiran Kumar Reddy
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - Saima Ghafoor Anjum
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - Hong Cao
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - Sripriya Chellappan
- Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Visvaldas Kairys
- Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Miguel X. Fernandes
- Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Michael K. Gilson
- Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - Tariq M. Rana
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - Bruce Tidor
- Department of Biological Engineering, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Kiran Kumar Reddy GS, Ali A, Nalam MNL, Anjum SG, Cao H, Nathans RS, Schiffer CA, Rana TM. Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2' ligands in pseudosymmetric dipeptide isosteres. J Med Chem 2007; 50:4316-28. [PMID: 17696512 PMCID: PMC3862176 DOI: 10.1021/jm070284z] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of novel HIV-1 protease inhibitors based on two pseudosymmetric dipeptide isosteres have been synthesized and evaluated. The inhibitors were designed by incorporating N-phenyloxazolidinone-5-carboxamides into the hydroxyethylene and (hydroxyethyl)hydrazine dipeptide isosteres as P2 and P2' ligands. Compounds with (S)-phenyloxazolidinones attached at a position proximal to the central hydroxyl group showed low nM inhibitory activities against wild-type HIV-1 protease. Selected compounds were further evaluated for their inhibitory activities against a panel of multidrug-resistant protease variants and for their antiviral potencies in MT-4 cells. The crystal structures of lopinavir (LPV) and two new inhibitors containing phenyloxazolidinone-based ligands in complex with wild-type HIV-1 protease have been determined. A comparison of the inhibitor-protease structures with the LPV-protease structure provides valuable insight into the binding mode of the new inhibitors to the protease enzyme. Based on the crystal structures and knowledge of structure-activity relationships, new inhibitors can be designed with enhanced enzyme inhibitory and antiviral potencies.
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Affiliation(s)
- G. S. Kiran Kumar Reddy
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Akbar Ali
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Saima Ghafoor Anjum
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Hong Cao
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Robin S. Nathans
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Tariq M. Rana
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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Chellappan S, Kiran Kumar Reddy GS, Ali A, Nalam MNL, Anjum SG, Cao H, Kairys V, Fernandes MX, Altman MD, Tidor B, Rana TM, Schiffer CA, Gilson MK. Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem Biol Drug Des 2007; 69:298-313. [PMID: 17539822 DOI: 10.1111/j.1747-0285.2007.00514.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
There is a clinical need for HIV protease inhibitors that can evade resistance mutations. One possible approach to designing such inhibitors relies upon the crystallographic observation that the substrates of HIV protease occupy a rather constant region within the binding site. In particular, it has been hypothesized that inhibitors which lie within this region will tend to resist clinically relevant mutations. The present study offers the first prospective evaluation of this hypothesis, via computational design of inhibitors predicted to conform to the substrate envelope, followed by synthesis and evaluation against wild-type and mutant proteases, as well as structural studies of complexes of the designed inhibitors with HIV protease. The results support the utility of the substrate envelope hypothesis as a guide to the design of robust protease inhibitors.
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Affiliation(s)
- Sripriya Chellappan
- Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, Rockville, MD 20850, USA
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Ali A, Reddy GSKK, Cao H, Anjum SG, Nalam MNL, Schiffer CA, Rana TM. Discovery of HIV-1 Protease Inhibitors with Picomolar Affinities Incorporating N-Aryl-oxazolidinone-5-carboxamides as Novel P2 Ligands. J Med Chem 2006; 49:7342-56. [PMID: 17149864 DOI: 10.1021/jm060666p] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Here, we describe the design, synthesis, and biological evaluation of novel HIV-1 protease inhibitors incorporating N-phenyloxazolidinone-5-carboxamides into the (hydroxyethylamino)sulfonamide scaffold as P2 ligands. Series of inhibitors with variations at the P2 phenyloxazolidinone and the P2' phenylsulfonamide moieties were synthesized. Compounds with the (S)-enantiomer of substituted phenyloxazolidinones at P2 show highly potent inhibitory activities against HIV-1 protease. The inhibitors possessing 3-acetyl, 4-acetyl, and 3-trifluoromethyl groups at the phenyl ring of the oxazolidinone fragment are the most potent in each series, with K(i) values in the low picomolar (pM) range. The electron-donating groups 4-methoxy and 1,3-dioxolane are preferred at P2' phenyl ring, as compounds with other substitutions show lower binding affinities. Attempts to replace the isobutyl group at P1' with small cyclic moieties caused significant loss of affinities in the resulting compounds. Crystal structure analysis of the two most potent inhibitors in complex with the HIV-1 protease provided valuable information on the interactions between the inhibitor and the protease enzyme. In both inhibitor - enzyme complexes, the carbonyl group of the oxazolidinone ring makes hydrogenbond interactions with relatively conserved Asp29 residue of the protease. Potent inhibitors from each series incorporating various phenyloxazolidinone based P2 ligands were selected and their activities against a panel of multidrug-resistant (MDR) protease variants were determined. Interestingly, the most potent protease inhibitor starts out with extremely tight affinity for the wild-type enzyme (K(i) = 0.8 pM), and even against the MDR variants it retains picomolar to low nanomolar K(i), which is highly comparable with the best FDA-approved protease inhibitors.
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Affiliation(s)
- Akbar Ali
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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