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Mons E, Kim RQ, Mulder MPC. Technologies for Direct Detection of Covalent Protein—Drug Adducts. Pharmaceuticals (Basel) 2023; 16:ph16040547. [PMID: 37111304 PMCID: PMC10146396 DOI: 10.3390/ph16040547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
In the past two decades, drug candidates with a covalent binding mode have gained the interest of medicinal chemists, as several covalent anticancer drugs have successfully reached the clinic. As a covalent binding mode changes the relevant parameters to rank inhibitor potency and investigate structure-activity relationship (SAR), it is important to gather experimental evidence on the existence of a covalent protein–drug adduct. In this work, we review established methods and technologies for the direct detection of a covalent protein–drug adduct, illustrated with examples from (recent) drug development endeavors. These technologies include subjecting covalent drug candidates to mass spectrometric (MS) analysis, protein crystallography, or monitoring intrinsic spectroscopic properties of the ligand upon covalent adduct formation. Alternatively, chemical modification of the covalent ligand is required to detect covalent adducts by NMR analysis or activity-based protein profiling (ABPP). Some techniques are more informative than others and can also elucidate the modified amino acid residue or bond layout. We will discuss the compatibility of these techniques with reversible covalent binding modes and the possibilities to evaluate reversibility or obtain kinetic parameters. Finally, we expand upon current challenges and future applications. Overall, these analytical techniques present an integral part of covalent drug development in this exciting new era of drug discovery.
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Affiliation(s)
- Elma Mons
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Robbert Q. Kim
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Monique P. C. Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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Radhika R, Shankar R, Vijayakumar S, Kolandaivel P. Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:1369-1401. [PMID: 28436311 DOI: 10.1080/07391102.2017.1323013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of -46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X-H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent's rule is verified for the C-H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (ρ) and Laplacian of electron density (∇2ρ) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT)4 with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA.
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Affiliation(s)
- R Radhika
- a Department of Physics , Bharathiar University , Coimbatore , India
| | - R Shankar
- a Department of Physics , Bharathiar University , Coimbatore , India
| | - S Vijayakumar
- b Department of Medical Physics , Bharathiar University , Coimbatore , India
| | - P Kolandaivel
- a Department of Physics , Bharathiar University , Coimbatore , India
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Salem AA, El Haty IA, Abdou IM, Mu Y. Interaction of human telomeric G-quadruplex DNA with thymoquinone: a possible mechanism for thymoquinone anticancer effect. Biochim Biophys Acta Gen Subj 2014; 1850:329-42. [PMID: 25450185 DOI: 10.1016/j.bbagen.2014.10.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 10/16/2014] [Accepted: 10/20/2014] [Indexed: 01/10/2023]
Abstract
BACKGROUND Thymoquinone (TQ) has been documented to possess chemo-preventive and chemotherapeutic antitumor effects. Studies reported that TQ inhibits the growth of cancer cells in animal models, culture and xenografted tumors. Molecular mechanisms underlying these anticancer effects were attributed to inductions of cell cycle arrest, apoptosis, oxidative damage of cellular macromolecules, blockade of tumor angiogenesis and inhibitions in migration, invasion and metastasis of cancer cells. On the other hand, human telomere DNA plays a role in regulating genes' transcriptions. It folds up into G-quadruplex structures that inhibit telomerase enzyme over-expressed in cancerous cells. Molecules that selectively stabilize G-quadruplex are potential anticancer agents. Therefore, this work aimed to explore the interaction of TQ with G-quadruplex DNA as a possible underlying mechanism for the anticancer effect of TQ. METHODS Interactions of TQ with telomeric G-quadruplex (5'-AGGG(TTAGGG)3-3') and duplex DNAs were studied using UV-vis, fluorescence, circular dichroism, liquid and solid NMR (1H and 13C), melting temperature and docking simulation. RESULTS Changes in UV-vis, CD, fluorescence, 1H NMR and 13C NMR, spectra as well as melting temperatures and docking simulations provided evidences for TQ's interactions with G-quadruplex. TQ was found to interact with G-quadruplex on two binding sites adjacent to the TTA loop with binding constants 1.80×10(5) and 1.12×10(7) M(-1). Melting temperatures indicated that TQ stabilized G-quadruplex by 5.6 °C and destabilized ct-DNA by 5.1 °C. Selectivity experiment indicated that TQ is preferentially binding to G-quadruplex over duplex with selectivity coefficients of 2.80-3.33×10(-3). Results suggested an intercalation binding mode based on π-π stacking. CONCLUSION Our results propose that TQ can possibly act as a G-quadruplex DNA stabilizer and subsequently contribute to the inhibition of telomerase enzyme and cancer's proliferation. GENERAL SIGNIFICANCE Our results represent a change in the paradigms reported for structural features of G-quadruplex's stabilizers and anticancer mechanisms of TQ.
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Affiliation(s)
- Alaa A Salem
- Department of Chemistry, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.
| | - Ismail A El Haty
- Department of Chemistry, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Ibrahim M Abdou
- Department of Chemistry, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Yuguang Mu
- School of Biological Sciences, College of Science, Nanyang Technological University, Singapore 637551, Singapore
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LaPlante SR, Bilodeau F, Aubry N, Gillard JR, O'Meara J, Coulombe R. N- versus O-alkylation: utilizing NMR methods to establish reliable primary structure determinations for drug discovery. Bioorg Med Chem Lett 2013; 23:4663-8. [PMID: 23809849 DOI: 10.1016/j.bmcl.2013.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 05/23/2013] [Accepted: 06/03/2013] [Indexed: 01/13/2023]
Abstract
A classic synthetic issue that remains unresolved is the reaction that involves the control of N- versus O-alkylation of ambident anions. This common chemical transformation is important for medicinal chemists, who require predictable and reliable protocols for the rapid synthesis of inhibitors. The uncertainty of whether the product(s) are N- and/or O-alkylated is common and can be costly if undetermined. Herein, we report an NMR-based strategy that focuses on distinguishing inhibitors and intermediates that are N- or O-alkylated. The NMR strategy involves three independent and complementary methods. However, any combination of two of the methods can be reliable if the third were compromised due to resonance overlap or other issues. The timely nature of these methods (HSQC/HMQC, HMBC. ROESY, and (13)C shift predictions) allows for contemporaneous determination of regioselective alkylation as needed during the optimization of synthetic routes.
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Affiliation(s)
- Steven R LaPlante
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd, 2100 Cunard St., Laval, Quebec H7S 2G5, Canada.
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Ahmadi F, Jafari B, Rahimi-Nasrabadi M, Ghasemi S, Ghanbari K. Proposed model for in vitro interaction between fenitrothion and DNA, by using competitive fluorescence, (31)P NMR, (1)H NMR, FT-IR, CD and molecular modeling. Toxicol In Vitro 2012; 27:641-50. [PMID: 23153512 DOI: 10.1016/j.tiv.2012.11.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 10/24/2012] [Accepted: 11/03/2012] [Indexed: 10/27/2022]
Abstract
In this work we proposed a model for in vitro interaction of fenitrothion (FEN) with calf thymus-DNA by combination of multispectroscopic and two dimensional molecular modeling (ONIOM) methods. The circular dichroism results showed that FEN changes the conformation of B-DNA and caused some changes to C-DNA form. The FT-IR results confirmed a partial intercalation between FEN and edges of all base pairs. The competitive fluorescence, using methylene blue as fluorescence probe, in the presence of increasing amounts of FEN, revealed that FEN is able to release the non-intercalated methylene blue from the DNA. The weak chemical shift and peak broadening of (1)H NMR spectrum of FEN in the presence of DNA confirmed a non-intercalation mode. The (31)P NMR showed that FEN interacts more with DNA via its -NO2 moiety. The ONIOM, based on the hybridization of QM/MM (DFT, 6.31++G (d,p)/UFF) methodology, was also performed by Gaussian 2003 package. The results revealed that the interaction is base sequence dependent, and FEN interacts more with AT base sequences.
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Affiliation(s)
- Farhad Ahmadi
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Abstract
Molecular docking, molecular mechanics, molecular dynamics and relaxation matrix simulation protocols have been extensively used to generate the structural details of ligand-receptor complexes in order to understand the binding interactions between the two entities. Experimental methods like NMR spectroscopy and X-ray crystallography are known to provide structural information about ligand-receptor complexes. In addition, fluorescence spectroscopy, circular dichroism (CD) spectroscopy and molecular docking have also been utilized to decode the phenomenon of the ligand-DNA interactions, with good correlation between experimental and computational results. The DNA binding affinity was demonstrated by analysing fluorescence spectral data. Structural rigidity of DNA upon ligand binding was identified by CD spectroscopy. Docking is carried out using the DNA-Dock program which results in the binding affinity data along with structural information like interatomic distances and H-bonding, etc. The complete structural analyses of various drug-DNA complexes have afforded results that indicate a specific DNA binding pattern of these ligands. It also exhibited that certain structural features of ligands can make a ligand to be AT- or GC-specific. It was also demonstrated that changing specificity from AT base pairs to GC base pairs further improved the DNA topoisomerase inhibiting activity in certain ligands. Thus, a specific molecular recognition signature encrypted in the structure of ligand can be decoded and can be effectively employed in designing more potent antiviral and antitumour agents.
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Interaction of polymyxin B with ds-DNA, and determination of DNA or polymyxin B via resonance Rayleigh scattering and resonance non-linear scattering spectra. Mikrochim Acta 2011. [DOI: 10.1007/s00604-011-0547-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13C-labeled indolequinone-DTPA-Gd conjugate for NMR probing cytochrome:P450 reductase-mediated one-electron reduction. Bioorg Med Chem Lett 2011; 21:790-3. [DOI: 10.1016/j.bmcl.2010.11.105] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 11/16/2010] [Accepted: 11/20/2010] [Indexed: 11/19/2022]
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Cherepanov AV, Glaubitz C, Schwalbe H. High-resolution studies of uniformly 13C,15N-labeled RNA by solid-state NMR spectroscopy. Angew Chem Int Ed Engl 2010; 49:4747-50. [PMID: 20533472 DOI: 10.1002/anie.200906885] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Alexey V Cherepanov
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438 Frankfurt, Germany
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Cherepanov A, Glaubitz C, Schwalbe H. Hochauflösende Festkörper-NMR-Spektroskopie an vollständig 13C,15N-markierter RNA. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906885] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Mielke SP, Krishnan V. Characterization of protein secondary structure from NMR chemical shifts. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2009; 54:141-165. [PMID: 20160946 PMCID: PMC2766081 DOI: 10.1016/j.pnmrs.2008.06.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Steven P. Mielke
- UC Davis Genome Center, University of California, Davis, California
| | - V.V. Krishnan
- Department of Applied Science and Center for Comparative Medicine, University of California, Davis, California
- Department of Chemistry, California State University, Fresno, California
- Correspondence to or
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Shen Z, Liu X, Zhou X, Liang A, Wu D, Yu L, Dai Z, Qin J, Lin B. Quantitative evaluation of the interaction between netropsin and double stranded oligodeoxynucleotides by microfabricated capillary array electrophoresis. J Sep Sci 2007; 30:1544-8. [PMID: 17623435 DOI: 10.1002/jssc.200600530] [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: 11/07/2022]
Abstract
Microfabricated capillary array electrophoresis (micro-CAE) was applied to study the interaction between minor groove binder netropsin and a non-selfcomplementary 12 mer double stranded oligodeoxynucleotide: d(CCCCTATACCGC).d(GCGGTATAGGGG). ESI-MS was used to provide an independent verification of the microchip electrophoresis derived data. Simultaneous parallel quantitative assay of multiple samples was performed in a single run (<50 s) on the self-developed micro-CAE device. The binding constant and stoichiometry calculated from Scatchard plot were (2.88 +/- 0.23)x10(5) M(-1) and 1:1, respectively. The values showed a good quantitative agreement with the results determined by ESI-MS and those using other methods reported in the literature.
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Affiliation(s)
- Zheng Shen
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
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Martini S, Bonechi C, Corbini G, Rossi C. Determination of the modified ‘affinity index’ of small ligands and macromolecular receptors from NMR spin-lattice relaxation data. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Lomozik L, Jastrzab R. Interference of Copper(II) ions with Non-covalent Interactions in Uridine or Uridine 5′-Monophosphate Systems with Adenosine, Cytidine, Thymidine and their Monophosphates in Aqueous Solution. J SOLUTION CHEM 2007. [DOI: 10.1007/s10953-006-9114-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Martini S, Bonechi C, Casolaro M, Corbini G, Rossi C. Drug–protein recognition processes investigated by NMR relaxation data. Biochem Pharmacol 2006; 71:858-64. [PMID: 16413504 DOI: 10.1016/j.bcp.2005.12.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Revised: 12/05/2005] [Accepted: 12/08/2005] [Indexed: 11/20/2022]
Abstract
In this paper we investigated the interaction processes occurring at the protein-solvent interface for prednisolone-albumin and prednisone-albumin systems, using an approach based on the analysis of proton selective relaxation rate enhancements of the ligand in the presence of the macromolecule. The contribution from the bound ligand fraction to the observed relaxation rate in relation to protein concentration allowed the calculation of the affinity index[A]L(T) and the normalized affinity index [AI(N)]L(T) which removes the effects of motional anisotropies and different proton densities, and isolates the contribution due to a decrease in the ligand dynamics caused by the binding with the protein. This approach allowed the comparison of the binding ability of prednisolone and prednisone towards albumin.
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Affiliation(s)
- Silvia Martini
- Department of Chemical and Biosystem Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
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Lomozik L, Jastrzab R. Noncovalent Interaction of Uridine 5′-Monophosphate with Adenosine, Cytidine, and Thymidine, as well as Adenosine 5′-Monophosphate and Cytidine 5′-Monophosphate in Aqueous Solution. J SOLUTION CHEM 2006. [DOI: 10.1007/s10953-006-9376-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lomozik L, Jastrzab R. Equilibrium and NMR Studies of Noncovalent Interactions in Binary Systems: Uridine, Adenosine, Cytidine and Thymidine, and Adenosine (or Cytidine) 5?-Monophosphate in Aqueous Solution. J SOLUTION CHEM 2004. [DOI: 10.1007/s10953-004-7138-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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