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Sarkar N, Banerjee J, Hanson AJ, Elegbede AI, Rosendahl T, Krueger AB, Banerjee AL, Tobwala S, Wang R, Lu X, Mallik S, Srivastava DK. Matrix Metalloproteinase-Assisted Triggered Release of Liposomal Contents. Bioconjug Chem 2007; 19:57-64. [DOI: 10.1021/bc070081p] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Nihar Sarkar
- Department of Pharmaceutical Sciences and Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, and Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
| | - Jayati Banerjee
- Department of Pharmaceutical Sciences and Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, and Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
| | - Andrea J. Hanson
- Department of Pharmaceutical Sciences and Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, and Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
| | - Adekunle I. Elegbede
- Department of Pharmaceutical Sciences and Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, and Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
| | - Theresa Rosendahl
- Department of Pharmaceutical Sciences and Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, and Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
| | - Aaron B. Krueger
- Department of Pharmaceutical Sciences and Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, and Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
| | - Abir L. Banerjee
- Department of Pharmaceutical Sciences and Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, and Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
| | - Shakila Tobwala
- Department of Pharmaceutical Sciences and Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, and Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
| | - Rongying Wang
- Department of Pharmaceutical Sciences and Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, and Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
| | - Xiaoning Lu
- Department of Pharmaceutical Sciences and Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, and Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
| | - Sanku Mallik
- Department of Pharmaceutical Sciences and Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, and Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
| | - D. K. Srivastava
- Department of Pharmaceutical Sciences and Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, and Proteomics Core Facility, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202
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Srivastava DK, Jude KM, Banerjee AL, Haldar M, Manokaran S, Kooren J, Mallik S, Christianson DW. Structural analysis of charge discrimination in the binding of inhibitors to human carbonic anhydrases I and II. J Am Chem Soc 2007; 129:5528-37. [PMID: 17407288 PMCID: PMC2532950 DOI: 10.1021/ja068359w] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [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: 11/28/2022]
Abstract
Despite the similarity in the active site pockets of carbonic anhydrase (CA) isozymes I and II, the binding affinities of benzenesulfonamide inhibitors are invariably higher with CA II as compared to CA I. To explore the structural basis of this molecular recognition phenomenon, we have designed and synthesized simple benzenesulfonamide inhibitors substituted at the para position with positively charged, negatively charged, and neutral functional groups, and we have determined the affinities and X-ray crystal structures of their enzyme complexes. The para-substituents are designed to bind in the midsection of the 15 A deep active site cleft, where interactions with enzyme residues and solvent molecules are possible. We find that a para-substituted positively charged amino group is more poorly tolerated in the active site of CA I compared with CA II. In contrast, a para-substituted negatively charged carboxylate substituent is tolerated equally well in the active sites of both CA isozymes. Notably, enzyme-inhibitor affinity increases upon neutralization of inhibitor charged groups by amidation or esterification. These results inform the design of short molecular linkers connecting the benzenesulfonamide group and a para-substituted tail group in "two-prong" CA inhibitors: an optimal linker segment will be electronically neutral, yet capable of engaging in at least some hydrogen bond interactions with protein residues and/or solvent. Microcalorimetric data reveal that inhibitor binding to CA I is enthalpically less favorable and entropically more favorable than inhibitor binding to CA II. This contrasting behavior may arise in part from differences in active site desolvation and the conformational entropy of inhibitor binding to each isozyme active site.
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Affiliation(s)
- D. K. Srivastava
- Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, ND 58105
| | - Kevin M. Jude
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
| | - Abir L. Banerjee
- Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, ND 58105
| | - Manas Haldar
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58105
| | - Sumathra Manokaran
- Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, ND 58105
| | - Joel Kooren
- Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, ND 58105
| | - Sanku Mallik
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58105
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
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Jude KM, Banerjee AL, Haldar MK, Manokaran S, Roy B, Mallik S, Srivastava DK, Christianson DW. Ultrahigh resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors reveal the molecular basis of high affinity. J Am Chem Soc 2006; 128:3011-8. [PMID: 16506782 PMCID: PMC2527509 DOI: 10.1021/ja057257n] [Citation(s) in RCA: 59] [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: 12/31/2022]
Abstract
The atomic-resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors are reported. Each inhibitor contains a benzenesulfonamide prong and a cupric iminodiacetate (IDA-Cu(2+)) prong separated by linkers of different lengths and compositions. The ionized NH(-) group of each benzenesulfonamide coordinates to the active site Zn(2+) ion; the IDA-Cu(2+) prong of the tightest-binding inhibitor, BR30, binds to H64 of CAII and H200 of CAI. This work provides the first evidence verifying the structural basis of nanomolar affinity measured for two-prong inhibitors targeting the carbonic anhydrases.
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Affiliation(s)
- Kevin M. Jude
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Abir L. Banerjee
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
| | - Manas K. Haldar
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816
| | - Sumathra Manokaran
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
| | - Bidhan Roy
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816
| | - Sanku Mallik
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816
| | - D. K. Srivastava
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Banerjee AL, Tobwala S, Ganguly B, Mallik S, Srivastava DK. Molecular basis for the origin of differential spectral and binding profiles of dansylamide with human carbonic anhydrase I and II. Biochemistry 2005; 44:3673-82. [PMID: 15751944 DOI: 10.1021/bi0475018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [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: 11/29/2022]
Abstract
Sulfonamide derivatives serve as potent inhibitors of carbonic anhydrases (CAs), and a few such inhibitors have been currently used as drugs for the treatment of different pathogenic conditions in humans. In pursuit of designing the isozyme-specific inhibitors of human CAs, we observed that the fluorescence spectral properties and binding profiles of a fluorogenic sulfonamide derivative, 5-(dimethylamino)-1-naphthalenesulfonamide (dansylamide, DNSA), were markedly different between the recombinant forms of human carbonic anhydrase I (hCA I) and II (hCA II). The kinetic evaluation of the overall microscopic pathways for the binding of DNSA to hCA I versus hCA II revealed that the protein isomerization step served as a major determinant of the above discrepancy. Arguments are presented that the detailed structural-functional investigations of enzyme-ligand interactions may provide insights into designing the isozyme-specific inhibitors of CAs.
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Affiliation(s)
- Abir L Banerjee
- Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, USA
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Banerjee AL, Eiler D, Roy BC, Jia X, Haldar MK, Mallik S, Srivastava DK. Spacer-based selectivity in the binding of "two-prong" ligands to recombinant human carbonic anhydrase I. Biochemistry 2005; 44:3211-24. [PMID: 15736932 DOI: 10.1021/bi047737b] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [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: 11/29/2022]
Abstract
Benzenesulfonamide and iminodiacetate (IDA)-conjugated Cu(2+) independently interact at the active site and a peripheral site of carbonic anhydrases, respectively [Banerjee, A. L., Swanson, M., Roy, B. C., Jia, X., Haldar, M. K., Mallik, S., and Srivastava, D. K. (2004) J. Am. Chem. Soc. 126, 10875-10883]. By attaching IDA-bound Cu(2+) to benzenesulfonamide via different chain length spacers, we synthesized two "two-prong" ligands, L1 and L2, in which the distances between Cu(2+) and NH(2) group of sulfonamide were 29 and 22 A, respectively. We compared the binding affinities of L1 and L2, vis-a-vis their parent compound, benzenesulfonamide, for recombinant human carbonic anhydrase I (hCA-I) by performing the fluorescence titration and steady-state kinetic experiments. The experimental data revealed that whereas the binding affinity of L1 for hCA-I was similar to that of benzenesulfonamide, the binding affinity of L2 was approximately 2 orders of magnitude higher, making L2 one of the most potent ligands or inhibitors of hCA-I. Since the enhanced binding or inhibitory potency of L2 is diminished (to the level of benzenesulfonamide) either in the presence of EDTA or upon treatment of the enzyme with diethyl pyrocarbonate, it is proposed that Cu(2+) of L2 interacts with one of the surface-exposed histidine residues of the enzyme. A cumulative account of the experimental data leads to the suggestion that the differential binding of L1 versus L2 to hCA-I is encoded in the chain length of the spacer moiety.
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Affiliation(s)
- Abir L Banerjee
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, USA
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Sarkar NR, Rosendahl T, Krueger AB, Banerjee AL, Benton K, Mallik S, Srivastava DK. "Uncorking" of liposomes by matrix metalloproteinase-9. Chem Commun (Camb) 2005:999-1001. [PMID: 15719095 DOI: 10.1039/b416827e] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [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: 11/21/2022]
Abstract
A triggered release methodology of liposomal contents via the enzyme MMP-9 is described.
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Affiliation(s)
- Nihar R Sarkar
- Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, USA.
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Banerjee AL, Tobwala S, Haldar MK, Swanson M, Roy BC, Mallik S, Srivastava DK. Inhibition of matrix metalloproteinase-9 by “multi-prong” surface binding groups. Chem Commun (Camb) 2005:2549-51. [PMID: 15900322 DOI: 10.1039/b501780g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [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: 01/25/2023]
Abstract
A novel strategy of blocking the active site accessibility of MMP-9 by "multi-prong" surface binding groups is described.
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Affiliation(s)
- Abir L Banerjee
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, ND 58105, USA
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Hanley PJ, Dröse S, Brandt U, Lareau RA, Banerjee AL, Srivastava DK, Banaszak LJ, Barycki JJ, Van Veldhoven PP, Daut J. 5-Hydroxydecanoate is metabolised in mitochondria and creates a rate-limiting bottleneck for beta-oxidation of fatty acids. J Physiol 2004; 562:307-18. [PMID: 15513944 PMCID: PMC1665522 DOI: 10.1113/jphysiol.2004.073932] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [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: 12/30/2022] Open
Abstract
5-Hydroxydecanoate (5-HD) blocks pharmacological and ischaemic preconditioning, and has been postulated to be a specific inhibitor of mitochondrial ATP-sensitive K(+) (K(ATP)) channels. However, recent work has shown that 5-HD is activated to 5-hydroxydecanoyl-CoA (5-HD-CoA), which is a substrate for the first step of beta-oxidation. We have now analysed the complete beta-oxidation of 5-HD-CoA using specially synthesised (and purified) substrates and enzymes, as well as isolated rat liver and heart mitochondria, and compared it with the metabolism of the physiological substrate decanoyl-CoA. At the second step of beta-oxidation, catalysed by enoyl-CoA hydratase, enzyme kinetics were similar using either decenoyl-CoA or 5-hydroxydecenoyl-CoA as substrate. The last two steps were investigated using l-3-hydroxyacyl-CoA dehydrogenase (HAD) coupled to 3-ketoacyl-CoA thiolase. V(max) for the metabolite of 5-HD (3,5-dihydroxydecanoyl-CoA) was fivefold slower than for the corresponding metabolite of decanoate (l-3-hydroxydecanoyl-CoA). The slower kinetics were not due to accumulation of d-3-hydroxyoctanoyl-CoA since this enantiomer did not inhibit HAD. Molecular modelling of HAD complexed with 3,5-dihydroxydecanoyl-CoA suggested that the 5-hydroxyl group could decrease HAD turnover rate by interacting with critical side chains. Consistent with the kinetic data, 5-hydroxydecanoyl-CoA alone acted as a weak substrate in isolated mitochondria, whereas addition of 100 mum 5-HD-CoA inhibited the metabolism of decanoyl-CoA or lauryl-carnitine. In conclusion, 5-HD is activated, transported into mitochondria and metabolised via beta-oxidation, albeit with rate-limiting kinetics at the penultimate step. This creates a bottleneck for beta-oxidation of fatty acids. The complex metabolic effects of 5-HD invalidate the use of 5-HD as a blocker of mitochondrial K(ATP) channels in studies of preconditioning.
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Affiliation(s)
- Peter J Hanley
- Institut für Normale und Pathologische Physiologie, Universität Marburg, Deutschhausstrasse 2, 35037 Marburg, Germany.
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Banerjee AL, Swanson M, Mallik S, Srivastava DK. Purification of recombinant human carbonic anhydrase-II by metal affinity chromatography without incorporating histidine tags. Protein Expr Purif 2004; 37:450-4. [PMID: 15358369 DOI: 10.1016/j.pep.2004.06.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [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] [Received: 05/10/2004] [Revised: 06/15/2004] [Indexed: 10/26/2022]
Abstract
Due to their involvement in diverse pathological conditions, carbonic anhydrases have been the targets of drug developments for the treatments of glaucoma, epilepsy, high altitude sickness, as well as cancer. Of about 14 isozymes of carbonic anhydrases, carbonic anhydrase-II (hCA-II) has been most extensively investigated from the structural, functional, and inhibitor design point of view. We discovered that hCA-II preferentially binds to the Sepharose-iminodiacetate (IDA)-Zn(2+) column, and such binding does not require incorporation of either N- or C-terminal histidine tags in the protein structure. By using the Sepharose-IDA-Zn(2+) affinity column, we purified the Escherichia coli expressed hCA-II with an overall recovery of 76%. The purified enzyme showed a single band on the SDS-PAGE. Due to ease in preparing the Sepharose-IDA-Zn(2+) column, and purifying hCA-II just in one step, the overall protocol will be ideal for producing bulk quantities of the enzyme for high throughput screening of inhibitors.
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Affiliation(s)
- Abir L Banerjee
- Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, ND 58105, USA
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Abstract
The enzyme inhibitors are usually designed by taking into consideration the overall dimensions of the enzyme's active site pockets. This conventional approach often fails to produce desirable affinities of inhibitors for their cognate enzymes. To circumvent such constraints, we contemplated enhancing the binding affinities of inhibitors by attaching tether groups, which would interact with the surface exposed amino acid residues. This strategy has been tested for the inhibition of human carbonic anhydrase II. Benzenesulfonamide serves as a weak inhibitor for the enzyme, but when it is conjugated to iminodiacetate-Cu2+ (which interacts with the surface-exposed His residues) via a spacer group, its binding affinity is enhanced by about 2 orders of magnitude. This "two-prong" approach is expected to serve as a general strategy for converting weak inhibitors of enzymes into tight-binding inhibitors.
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Affiliation(s)
- Bidhan C Roy
- Department of Chemistry, Biochemistry & Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, USA
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Banerjee AL, Swanson M, Roy BC, Jia X, Haldar MK, Mallik S, Srivastava DK. Protein surface-assisted enhancement in the binding affinity of an inhibitor for recombinant human carbonic anhydrase-II. J Am Chem Soc 2004; 126:10875-83. [PMID: 15339172 DOI: 10.1021/ja047557p] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [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
We elaborate on a novel strategy for enhancing the binding affinity of an active-site directed inhibitor by attaching a tether group, designed to interact with the surface-exposed histidine residue(s) of enzymes. In this approach, we have utilized the recombinant form of human carbonic anhydrase-II (hCA-II) as the enzyme source and benzenesulfonamide and its derivatives as inhibitors. The steady-state kinetic and the ligand binding data revealed that the attachment of iminodiacetate (IDA)-Cu(2+) to benzenesulfonamide (via a triethylene glycol spacer) enhanced its binding affinity for hCA-II by about 40-fold. No energetic contribution of either IDA or triethylene glycol spacer was found (at least in the ground state of the enzyme-inhibitor complex) when Cu(2+) was stripped off from the tether group-conjugated sulfonamide derivative. Arguments are presented that the overall strategy of enhancing the binding affinities of known inhibitors by attaching the IDA-Cu(2+) groups to interact with the surface-exposed histidine residues will find a general application in designing the isozyme-specific inhibitors as potential drugs.
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Affiliation(s)
- Abir L Banerjee
- Contribution from the Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, ND 58105, USA
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