1
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Jovanovic D, Poliyodath Mohanan M, Huber SM. Halogen, Chalcogen, Pnictogen, and Tetrel Bonding in Non-Covalent Organocatalysis: An Update. Angew Chem Int Ed Engl 2024; 63:e202404823. [PMID: 38728623 DOI: 10.1002/anie.202404823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/12/2024]
Abstract
The use of noncovalent interactions based on electrophilic halogen, chalcogen, pnictogen, or tetrel centers in organocatalysis has gained noticeable attention. Herein, we provide an overview on the most important developments in the last years with a clear focus on experimental studies and on catalysts which act via such non-transient interactions.
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Affiliation(s)
- Dragana Jovanovic
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Meghana Poliyodath Mohanan
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Stefan M Huber
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
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2
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Cristiano N, Cabayé A, Brabet I, Glatthar R, Tora A, Goudet C, Bertrand HO, Goupil-Lamy A, Flor PJ, Pin JP, McCort-Tranchepain I, Acher FC. Novel Inhibitory Site Revealed by XAP044 Mode of Action on the Metabotropic Glutamate 7 Receptor Venus Flytrap Domain. J Med Chem 2024; 67:11662-11687. [PMID: 38691510 DOI: 10.1021/acs.jmedchem.3c01924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Metabotropic glutamate (mGlu) receptors play a key role in modulating most synapses in the brain. The mGlu7 receptors inhibit presynaptic neurotransmitter release and offer therapeutic possibilities for post-traumatic stress disorders or epilepsy. Screening campaigns provided mGlu7-specific allosteric modulators as the inhibitor XAP044 (Gee et al. J. Biol. Chem. 2014). In contrast to other mGlu receptor allosteric modulators, XAP044 does not bind in the transmembrane domain but to the extracellular domain of the mGlu7 receptor and not at the orthosteric site. Here, we identified the mode of action of XAP044, combining synthesis of derivatives, modeling and docking experiments, and mutagenesis. We propose a unique mode of action of these inhibitors, preventing the closure of the Venus flytrap agonist binding domain. While acting as a noncompetitive antagonist of L-AP4, XAP044 and derivatives act as apparent competitive antagonists of LSP4-2022. These data revealed more potent XAP044 analogues and new possibilities to target mGluRs.
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Affiliation(s)
- Nunzia Cristiano
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS UMR 8601, 75006 Paris, France
| | - Alexandre Cabayé
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS UMR 8601, 75006 Paris, France
- BIOVIA Dassault Systèmes, F-78140 Vélizy-Villacoublay Cedex, France
| | - Isabelle Brabet
- Institute of Functional Genomics, University of Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | - Ralf Glatthar
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | - Amelie Tora
- Institute of Functional Genomics, University of Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | - Cyril Goudet
- Institute of Functional Genomics, University of Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | | | - Anne Goupil-Lamy
- BIOVIA Dassault Systèmes, F-78140 Vélizy-Villacoublay Cedex, France
| | - Peter J Flor
- Laboratory of Molecular and Cellular Neurobiology, Faculty of Biology and Preclinical Medicine, University of Regensburg, 93053 Regensburg, Germany
| | - Jean-Philippe Pin
- Institute of Functional Genomics, University of Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | - Isabelle McCort-Tranchepain
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS UMR 8601, 75006 Paris, France
| | - Francine C Acher
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS UMR 8601, 75006 Paris, France
- Saints-Pères Paris Institute for the Neurosciences, Université Paris Cité, CNRS UMR 8003, 75006 Paris, France
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3
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Kalabekova R, Quinn CM, Movellan KT, Gronenborn AM, Akke M, Polenova T. 19F Fast Magic-Angle Spinning NMR Spectroscopy on Microcrystalline Complexes of Fluorinated Ligands and the Carbohydrate Recognition Domain of Galectin-3. Biochemistry 2024. [PMID: 39008798 DOI: 10.1021/acs.biochem.4c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Structural characterization of protein-ligand binding interfaces at atomic resolution is essential for improving the design of specific and potent inhibitors. Herein, we explored fast 19F- and 1H-detected magic angle spinning NMR spectroscopy to investigate the interaction between two fluorinated ligand diastereomers with the microcrystalline galectin-3 carbohydrate recognition domain. The detailed environment around the fluorine atoms was mapped by 2D 13C-19F and 1H-19F dipolar correlation experiments and permitted characterization of the binding interface. Our results demonstrate that 19F MAS NMR is a powerful tool for detailed characterization of protein-ligand interfaces and protein interactions at the atomic level.
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Affiliation(s)
- Roza Kalabekova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Kumar Tekwani Movellan
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Angela M Gronenborn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261, United States
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, Lund SE-22100, Sweden
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261, United States
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4
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Wang S, Gan L, Han L, Deng P, Li Y, He D, Chi H, Zhu L, Li Y, Long R, Gan Z. Design, synthesis, and biological evaluation of naphthalene imidazo[1,2-b]pyridazine hybrid derivatives as VEGFR selective inhibitors. Arch Pharm (Weinheim) 2024:e2400411. [PMID: 39008876 DOI: 10.1002/ardp.202400411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/17/2024]
Abstract
The vascular endothelial growth factor receptor (VEGFR) is a receptor tyrosine kinase that is regarded as an emerging target for abnormal angiogenesis diseases. In this study, novel naphthalene imidazo[1,2-b]pyridazine hybrids as VEGFR selective inhibitors were designed and synthesized using a scaffold hopping strategy based on ponatinib, a multitarget kinase inhibitor. Among the evaluated compounds, derivative 9k (WS-011) demonstrated the most potent inhibitory potency against VEGFR-2 (IC50 = 8.4 nM) and displayed superior VEGFR selectivity over a panel of 70 kinases compared with ponatinib. Furthermore, 9k possessed good cytotoxic effects on various cancer cell lines, especially the colon cancer HT-29 cells, with an acceptable oral bioavailability. Moreover, 9k significantly inhibited the migration and invasion of human umbilical vein endothelial cells (HUVEC) cells and induced apoptosis through the upregulation of apoptotic proteins in HT-29 cells. 9k also effectively suppressed the activation of VEGFR-2 signaling pathways, which in turn inhibited the growth of HT-29 cells and the tube formation of HUVECs in vitro. All of the findings revealed that 9k could be considered a promising antiangiogenesis lead that merits further investigation.
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Affiliation(s)
- Shuang Wang
- Department of Medicinal Chemistry, College of Pharmacy, Chongqing Medical University, Chongqing, People's Republic of China
| | - LinLing Gan
- Chongqing Engineering Research Center of Pharmaceutical Sciences, School of Pharmacy, Chongqing Medical and Pharmaceutical College, Chongqing, People's Republic of China
| | - Lei Han
- Department of Medicinal Chemistry, College of Pharmacy, Chongqing Medical University, Chongqing, People's Republic of China
| | - Ping Deng
- Department of Medicinal Chemistry, College of Pharmacy, Chongqing Medical University, Chongqing, People's Republic of China
| | - Yihao Li
- Department of Medicinal Chemistry, College of Pharmacy, Chongqing Medical University, Chongqing, People's Republic of China
| | - Dongxiao He
- Department of Medicinal Chemistry, College of Pharmacy, Chongqing Medical University, Chongqing, People's Republic of China
| | - Haoze Chi
- Department of Medicinal Chemistry, College of Pharmacy, Chongqing Medical University, Chongqing, People's Republic of China
| | - Liwei Zhu
- Department of Medicinal Chemistry, College of Pharmacy, Chongqing Medical University, Chongqing, People's Republic of China
| | - Yuehui Li
- Department of Medicinal Chemistry, College of Pharmacy, Chongqing Medical University, Chongqing, People's Republic of China
| | - Rui Long
- Department of Pharmacy, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Zongjie Gan
- Department of Medicinal Chemistry, College of Pharmacy, Chongqing Medical University, Chongqing, People's Republic of China
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5
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Hahm G, Redeker FA, Jorabchi K. Multielement Detection of Nonmetals by Barium-Based Post-ICP Chemical Ionization Coupled to Orbitrap-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:871-882. [PMID: 38650348 PMCID: PMC11066957 DOI: 10.1021/jasms.3c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Prevalence of F, Cl, S, P, Br, and I in pharmaceuticals and environmental contaminants has promoted standard-free quantitation using analyte-independent heteroatom responses in inductively coupled plasma (ICP)-MS. However, in-plasma ionization challenges and element-dependent isobaric interference removal methods have hampered the multielement nonmetal detection in ICP-MS. Here, we examine an alternative approach to enhance multielement detection capabilities. Analytes are introduced into an ICP leading to post-plasma formation of HF, HCl, H3PO3, H2SO4, HBr, and HI, which are then chemically ionized to BaF+, BaCl+, BaH2PO3+, BaHSO4+, BaBr+, and BaI+ via reactions with barium-containing ions supplied by a nanospray. Subsequent ion detection by high-resolution MS provides an element-independent approach for resolving isobaric interferences. We show that elemental response factors using these ions are linear within 2 orders of magnitude and independent of analytes' chemical structures. Using a single set of operating parameters, detection limits <1 ng/mL are obtained for Cl, Br, I, and P, while those for F and S are 1.8 and 6.2 ng/mL, respectively, offering improved multielement quantitation of nonmetals. Further, insights into ionization mechanisms indicate that the reactivities of reagent ions follow the order BaNO2+ > BaHCO2+ > Ba(H2O)n2+ ∼ BaCH3CO2+. Notably, the least reactive ions are generated directly by nanospray, suggesting that modification of these ions via interaction with plasma afterglow is critical for achieving good sensitivities. Moreover, our experiments indicate that the element-specific plasma products follow the order HF < H2SO4 ∼ HCl < H3PO3 ∼ HBr ∼ HI for their propensity to react with reagent ions. These insights provide guidelines to manage matrix effects and offer pathways to further improve the technique.
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Affiliation(s)
- Grace Hahm
- Department of Chemistry, Georgetown
University, Washington, D.C. 20057, United States
| | - Frenio A. Redeker
- Department of Chemistry, Georgetown
University, Washington, D.C. 20057, United States
| | - Kaveh Jorabchi
- Department of Chemistry, Georgetown
University, Washington, D.C. 20057, United States
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6
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Klimt M, Stadler M, Binder U, Krauss J. Synthesis of novel benzylamine antimycotics and evaluation of their antimycotic potency. Arch Pharm (Weinheim) 2024; 357:e2300381. [PMID: 38345272 DOI: 10.1002/ardp.202300381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 05/08/2024]
Abstract
A series of 23 novel benzylamines was synthesized by reductive amination from halogen-substituted 3- and 4-benzyloxybenzaldehyde derivatives and 6-methylhept-2-yl amine or n-octylamine. The antimycotic activity of the resulting amines was evaluated in a microdilution assay against the apathogenic yeast Yarrowia lipolytica as test microorganism. Promising compounds were also tested against human pathogenic Candida species. The influence of halogen substituents at the benzyl ether side chain was studied in this screening, as well as the influence of the branched side chain of (±)-6-methylhept-2-yl amine in comparison with the n-octyl side chain.
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Affiliation(s)
- Monika Klimt
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Martina Stadler
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Ulrike Binder
- Department of Hygiene, Microbiology and Public Health, Institute of Hygiene and Medical Microbiology, Medical University Innsbruck, Innsbruck, Austria
| | - Jürgen Krauss
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-University Munich, Munich, Germany
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7
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Mizuguchi M, Nakagawa Y, Yokoyama T, Okada T, Fujii K, Takahashi K, Luan NNT, Nabeshima Y, Kanamitsu K, Nakagawa S, Yamakawa S, Ueda M, Ando Y, Toyooka N. Development of Benziodarone Analogues with Enhanced Potency for Selective Binding to Transthyretin in Human Plasma. J Med Chem 2024; 67:6987-7005. [PMID: 38670538 PMCID: PMC11089511 DOI: 10.1021/acs.jmedchem.3c02286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/31/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024]
Abstract
Transthyretin amyloidosis is a fatal disorder caused by transthyretin amyloid aggregation. Stabilizing the native structure of transthyretin is an effective approach to inhibit amyloid aggregation. To develop kinetic stabilizers of transthyretin, it is crucial to explore compounds that selectively bind to transthyretin in plasma. Our recent findings demonstrated that the uricosuric agent benziodarone selectively binds to transthyretin in plasma. Here, we report the development of benziodarone analogues with enhanced potency for selective binding to transthyretin in plasma compared to benziodarone. These analogues featured substituents of chlorine, bromine, iodine, a methyl group, or a trifluoromethyl group, at the 4-position of the benzofuran ring. X-ray crystal structure analysis revealed that CH···O hydrogen bonds and a halogen bond are important for the binding of the compounds to the thyroxine-binding sites. The bioavailability of benziodarone analogues with 4-Br, 4-Cl, or 4-CH3 was comparable to that of tafamidis, a current therapeutic agent for transthyretin amyloidosis.
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Affiliation(s)
- Mineyuki Mizuguchi
- Faculty
of Pharmaceutical Sciences, University of
Toyama, Toyama 930-0194, Japan
| | - Yusuke Nakagawa
- Graduate
School of Innovative Life Science, University
of Toyama, Toyama 930-8555, Japan
| | - Takeshi Yokoyama
- Faculty
of Pharmaceutical Sciences, University of
Toyama, Toyama 930-0194, Japan
| | - Takuya Okada
- Graduate
School of Innovative Life Science, University
of Toyama, Toyama 930-8555, Japan
- Faculty
of Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Kanako Fujii
- Graduate
School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Kanoko Takahashi
- Graduate
School of Pharma-Medical Sciences, University
of Toyama, Toyama 930-8555, Japan
| | - Nguyen Ngoc Thanh Luan
- Graduate
School of Innovative Life Science, University
of Toyama, Toyama 930-8555, Japan
| | - Yuko Nabeshima
- Faculty
of Pharmaceutical Sciences, University of
Toyama, Toyama 930-0194, Japan
| | - Kayoko Kanamitsu
- Graduate
School of Pharmaceutical Sciences, the University
of Tokyo, Tokyo 113-0033, Japan
| | - Shinsaku Nakagawa
- Graduate
School of Pharmaceutical Sciences, Osaka
University, Osaka 565-0871, Japan
| | - Shiori Yamakawa
- Department
of Neurology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Mitsuharu Ueda
- Department
of Neurology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yukio Ando
- Faculty
of Pharmaceutical Sciences, Nagasaki International
University, Sasebo 859-3298, Japan
| | - Naoki Toyooka
- Graduate
School of Innovative Life Science, University
of Toyama, Toyama 930-8555, Japan
- Faculty
of Engineering, University of Toyama, Toyama 930-8555, Japan
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8
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Brosey CA, Link TM, Shen R, Moiani D, Burnett K, Hura GL, Jones DE, Tainer JA. Chemical screening by time-resolved X-ray scattering to discover allosteric probes. Nat Chem Biol 2024:10.1038/s41589-024-01609-1. [PMID: 38671223 DOI: 10.1038/s41589-024-01609-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 03/20/2024] [Indexed: 04/28/2024]
Abstract
Drug discovery relies on efficient identification of small-molecule leads and their interactions with macromolecular targets. However, understanding how chemotypes impact mechanistically important conformational states often remains secondary among high-throughput discovery methods. Here, we present a conformational discovery pipeline integrating time-resolved, high-throughput small-angle X-ray scattering (TR-HT-SAXS) and classic fragment screening applied to allosteric states of the mitochondrial import oxidoreductase apoptosis-inducing factor (AIF). By monitoring oxidized and X-ray-reduced AIF states, TR-HT-SAXS leverages structure and kinetics to generate a multidimensional screening dataset that identifies fragment chemotypes allosterically stimulating AIF dimerization. Fragment-induced dimerization rates, quantified with time-resolved SAXS similarity analysis (kVR), capture structure-activity relationships (SAR) across the top-ranked 4-aminoquinoline chemotype. Crystallized AIF-aminoquinoline complexes validate TR-SAXS-guided SAR, supporting this conformational chemotype for optimization. AIF-aminoquinoline structures and mutational analysis reveal active site F482 as an underappreciated allosteric stabilizer of AIF dimerization. This conformational discovery pipeline illustrates TR-HT-SAXS as an effective technology for targeting chemical leads to important macromolecular states.
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Affiliation(s)
- Chris A Brosey
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Todd M Link
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Runze Shen
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Davide Moiani
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathryn Burnett
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Greg L Hura
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Darin E Jones
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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9
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Madhav H, Reddy GS, Rizvi Z, Jameel E, Patel TS, Rahman A, Yadav V, Fatima S, Heyat F, Pal K, Minju-Op A, Subbarao N, Bhattacharjee S, Dixit BC, Sijwali PS, Hoda N. Reinvestigation of diphenylmethylpiperazine analogues of pyrazine as new class of Plasmodial cysteine protease inhibitors for the treatment of malaria. RSC Med Chem 2024; 15:1022-1037. [PMID: 38516592 PMCID: PMC10953474 DOI: 10.1039/d3md00490b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/19/2023] [Indexed: 03/23/2024] Open
Abstract
Malaria eradication is still a global challenge due to the lack of a broadly effective vaccine and the emergence of drug resistance to most of the currently available drugs as part of the mainline artemisinin-based combination therapy. A variety of experimental approaches are quite successful in identifying and synthesizing new promising pharmacophore hybrids with distinct mechanisms of action. Based on our recent findings, the current study demonstrates the reinvestigation of a series of diphenylmethylpiperazine and pyrazine-derived molecular hybrids. Pyrazine-derived molecular hybrids were screened to investigate the antiplasmodial activity on drug-susceptible Pf3D7 and drug-resistant PfW2 strains. The selected compounds were shown to be potent dual inhibitors of cysteine protease PfFP2 and PfFP3. Time-course parasitic development study demonstrated that compounds were able to arrest the growth of the parasite at the early trophozoite stage. The compounds did not show hemolysis of red blood cells and showed selectivity to the parasite compared with the mammalian Vero and A5489 cell lines. The study underlined HR5 and HR15 as a new class of Plasmodial falcipain inhibitors with an IC50 of 6.2 μM and 5.9 μM for PfFP2 and 6.8 μM and 6.4 μM for PfFP3, respectively. Both compounds have antimalarial efficacy with IC50 values of 3.05 μM and 2.80 μM for the Pf3D7 strain, and 4.35 μM and 3.39 μM for the PfW2 strain, respectively. Further structural optimization may turn them into potential Plasmodial falcipain inhibitors for malaria therapeutics.
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Affiliation(s)
- Hari Madhav
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University) New Delhi-110025 India
| | - G Srinivas Reddy
- CSIR-Centre for Cellular and Molecular Biology Hyderabad-500007 TS India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 UP India
| | - Zeba Rizvi
- CSIR-Centre for Cellular and Molecular Biology Hyderabad-500007 TS India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 UP India
| | - Ehtesham Jameel
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University) New Delhi-110025 India
| | - Tarosh S Patel
- Chemistry Department, V. P. & R. P. T. P Science College, Affiliated to Sardar Patel University Vallabh Vidyanagar-388120 Gujarat India
| | - Abdur Rahman
- Special Centre for Molecular Medicine, Jawaharlal Nehru University New Delhi-110067 India
| | - Vikas Yadav
- School of Computational and Integrative Sciences, Jawaharlal Nehru University New Delhi-110067 India
| | - Sadaf Fatima
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University) New Delhi-110025 India
| | - Fatima Heyat
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University) New Delhi-110025 India
| | - Kavita Pal
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University) New Delhi-110025 India
| | - Amisha Minju-Op
- CSIR-Centre for Cellular and Molecular Biology Hyderabad-500007 TS India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University New Delhi-110067 India
| | - Souvik Bhattacharjee
- Special Centre for Molecular Medicine, Jawaharlal Nehru University New Delhi-110067 India
| | - Bharat C Dixit
- CSIR-Centre for Cellular and Molecular Biology Hyderabad-500007 TS India
| | - Puran Singh Sijwali
- CSIR-Centre for Cellular and Molecular Biology Hyderabad-500007 TS India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 UP India
| | - Nasimul Hoda
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University) New Delhi-110025 India
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10
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Huo T, Zhao X, Cheng Z, Wei J, Zhu M, Dou X, Jiao N. Late-stage modification of bioactive compounds: Improving druggability through efficient molecular editing. Acta Pharm Sin B 2024; 14:1030-1076. [PMID: 38487004 PMCID: PMC10935128 DOI: 10.1016/j.apsb.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/14/2023] [Accepted: 11/13/2023] [Indexed: 03/17/2024] Open
Abstract
Synthetic chemistry plays an indispensable role in drug discovery, contributing to hit compounds identification, lead compounds optimization, candidate drugs preparation, and so on. As Nobel Prize laureate James Black emphasized, "the most fruitful basis for the discovery of a new drug is to start with an old drug"1. Late-stage modification or functionalization of drugs, natural products and bioactive compounds have garnered significant interest due to its ability to introduce diverse elements into bioactive compounds promptly. Such modifications alter the chemical space and physiochemical properties of these compounds, ultimately influencing their potency and druggability. To enrich a toolbox of chemical modification methods for drug discovery, this review focuses on the incorporation of halogen, oxygen, and nitrogen-the ubiquitous elements in pharmacophore components of the marketed drugs-through late-stage modification in recent two decades, and discusses the state and challenges faced in these fields. We also emphasize that increasing cooperation between chemists and pharmacists may be conducive to the rapid discovery of new activities of the functionalized molecules. Ultimately, we hope this review would serve as a valuable resource, facilitating the application of late-stage modification in the construction of novel molecules and inspiring innovative concepts for designing and building new drugs.
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Affiliation(s)
- Tongyu Huo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xinyi Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zengrui Cheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jialiang Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Changping Laboratory, Beijing 102206, China
| | - Minghui Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiaodong Dou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Changping Laboratory, Beijing 102206, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, East China Normal University, Shanghai 200062, China
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11
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Jin R, Wang J, Li M, Tang T, Feng Y, Zhou S, Xie H, Feng H, Guo J, Fu R, Liu J, Tang Y, Shi Y, Guo H, Wang Y, Nie F, Li J. Discovery of a Novel Benzothiadiazine-Based Selective Aldose Reductase Inhibitor as Potential Therapy for Diabetic Peripheral Neuropathy. Diabetes 2024; 73:497-510. [PMID: 38127948 DOI: 10.2337/db23-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
Aldose reductase 2 (ALR2), an activated enzyme in the polyol pathway by hyperglycemia, has long been recognized as one of the most promising targets for complications of diabetes, especially in diabetic peripheral neuropathy (DPN). However, many of the ALR2 inhibitors have shown serious side effects due to poor selectivity over aldehyde reductase (ALR1). Herein, we describe the discovery of a series of benzothiadiazine acetic acid derivatives as potent and selective inhibitors against ALR2 and evaluation of their anti-DPN activities in vivo. Compound 15c, carrying a carbonyl group at the 3-position of the thiadiazine ring, showed high potent inhibition against ALR2 (IC50 = 33.19 nmol/L) and ∼16,109-fold selectivity for ALR2 over ALR1. Cytotoxicity assays ensured the primary biosafety of 15c. Further pharmacokinetic assay in rats indicated that 15c had a good pharmacokinetic feature (t1/2 = 5.60 h, area under the plasma concentration time curve [AUC(0-t)] = 598.57 ± 216.5 μg/mL * h), which was superior to epalrestat (t1/2 = 2.23 h, AUC[0-t] = 20.43 ± 3.7 μg/mL * h). Finally, in a streptozotocin-induced diabetic rat model, 15c significantly increased the nerve conduction velocities of impaired sensory and motor nerves, achieved potent inhibition of d-sorbitol production in the sciatic nerves, and significantly increased the paw withdrawal mechanical threshold. By combining the above investigations, we propose that 15c might represent a promising lead compound for the discovery of an antidiabetic peripheral neuropathy drug. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Ruyi Jin
- Shaanxi Key Lab Basic & New Herbal Medicament Research Center, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
- Shenzhen Neptunus Pharmaceutical Research Institute Co., Ltd., Shenzhen, China
| | - Jin Wang
- Shenzhen Neptunus Pharmaceutical Research Institute Co., Ltd., Shenzhen, China
- Shenzhen Huahong Marine Biomedicine Co. Ltd., Shenzhen, China
| | - Mingyue Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Tian Tang
- Shenzhen Neptunus Pharmaceutical Research Institute Co., Ltd., Shenzhen, China
- Cali Biosciences, Shenzhen, China
| | - Yidong Feng
- Shenzhen Neptunus Pharmaceutical Research Institute Co., Ltd., Shenzhen, China
| | - Sha Zhou
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry, Nankai University, Tianjin, China
| | - Honglei Xie
- School of Pharmacy, Shandong First Medical University and Shandong Academy of Medical Sciences, Yantai, China
| | - Haiyu Feng
- Shaanxi Key Lab Basic & New Herbal Medicament Research Center, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Jianshuang Guo
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Ruijia Fu
- Shaanxi Key Lab Basic & New Herbal Medicament Research Center, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Jiping Liu
- Shaanxi Key Lab Basic & New Herbal Medicament Research Center, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Yuping Tang
- Shaanxi Key Lab Basic & New Herbal Medicament Research Center, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Yajun Shi
- Shaanxi Key Lab Basic & New Herbal Medicament Research Center, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Hui Guo
- Shaanxi Key Lab Basic & New Herbal Medicament Research Center, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Yuwei Wang
- Shaanxi Key Lab Basic & New Herbal Medicament Research Center, College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Fayi Nie
- Shaanxi Key Laboratory of Acupuncture and Medicine, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Jing Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry, Nankai University, Tianjin, China
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12
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Chen S, Jin C, Ohgaki R, Xu M, Okanishi H, Kanai Y. Structure-activity characteristics of phenylalanine analogs selectively transported by L-type amino acid transporter 1 (LAT1). Sci Rep 2024; 14:4651. [PMID: 38409393 PMCID: PMC10897196 DOI: 10.1038/s41598-024-55252-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024] Open
Abstract
L-type amino acid transporter 1 (LAT1) is a transmembrane protein responsible for transporting large neutral amino acids. While numerous LAT1-targeted compound delivery for the brain and tumors have been investigated, their LAT1 selectivity often remains ambiguous despite high LAT1 affinity. This study assessed the LAT1 selectivity of phenylalanine (Phe) analogs, focusing on their structure-activity characteristics. We discovered that 2-iodo-L-phenylalanine (2-I-Phe), with an iodine substituent at position 2 in the benzene ring, markedly improves LAT1 affinity and selectivity compared to parent amino acid Phe, albeit at the cost of reduced transport velocity. L-Phenylglycine (Phg), one carbon shorter than Phe, was found to be a substrate for LAT1 with a lower affinity, exhibiting a low level of selectivity for LAT1 equivalent to Phe. Notably, (R)-2-amino-1,2,3,4-tetrahydro-2-naphthoic acid (bicyclic-Phe), with an α-methylene moiety akin to the α-methyl group in α-methyl-L-phenylalanine (α-methyl-Phe), a known LAT1-selective compound, showed similar LAT1 transport maximal velocity to α-methyl-Phe, but with higher LAT1 affinity and selectivity. In vivo studies revealed tumor-specific accumulation of bicyclic-Phe, underscoring the importance of LAT1-selectivity in targeted delivery. These findings emphasize the potential of bicyclic-Phe as a promising LAT1-selective component, providing a basis for the development of LAT1-targeting compounds based on its structural framework.
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Affiliation(s)
- Sihui Chen
- Department of Bio-System Pharmacology, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Chunhuan Jin
- Department of Bio-System Pharmacology, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryuichi Ohgaki
- Department of Bio-System Pharmacology, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Minhui Xu
- Department of Bio-System Pharmacology, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroki Okanishi
- Department of Bio-System Pharmacology, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshikatsu Kanai
- Department of Bio-System Pharmacology, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, 565-0871, Japan.
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, 565-0871, Japan.
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13
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Ma M, Zhang X, Zhou L, Han Z, Shi Y, Li J, Wu L, Xu Z, Zhu W. D3Rings: A Fast and Accurate Method for Ring System Identification and Deep Generation of Drug-Like Cyclic Compounds. J Chem Inf Model 2024; 64:724-736. [PMID: 38206320 DOI: 10.1021/acs.jcim.3c01657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Continuous exploration of the chemical space of molecules to find ligands with high affinity and specificity for specific targets is an important topic in drug discovery. A focus on cyclic compounds, particularly natural compounds with diverse scaffolds, provides important insights into novel molecular structures for drug design. However, the complexity of their ring structures has hindered the applicability of widely accepted methods and software for the systematic identification and classification of cyclic compounds. Herein, we successfully developed a new method, D3Rings, to identify acyclic, monocyclic, spiro ring, fused and bridged ring, and cage ring compounds, as well as macrocyclic compounds. By using D3Rings, we completed the statistics of cyclic compounds in three different databases, e.g., ChEMBL, DrugBank, and COCONUT. The results demonstrated the richness of ring structures in natural products, especially spiro, macrocycles, and fused and bridged rings. Based on this, three deep generative models, namely, VAE, AAE, and CharRNN, were trained and used to construct two data sets similar to DrugBank and COCONUT but 10 times larger than them. The enlarged data sets were then used to explore the molecular chemical space, focusing on complex ring structures, for novel drug discovery and development. Docking experiments with the newly generated COCONUT-like data set against three SARS-CoV-2 target proteins revealed that an expanded compound database improves molecular docking results. Cyclic structures exhibited the best docking scores among the top-ranked docking molecules. These results suggest the importance of exploring the chemical space of structurally novel cyclic compounds and continuous expansion of the library of drug-like compounds to facilitate the discovery of potent ligands with high binding affinity to specific targets. D3Rings is now freely available at http://www.d3pharma.com/D3Rings/.
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Affiliation(s)
- Minfei Ma
- Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinben Zhang
- Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Liping Zhou
- Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zijian Han
- Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yulong Shi
- Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jintian Li
- Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leyun Wu
- Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Xu
- Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- Stake Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Yssartier T, Liu L, Pardoue S, Le Questel JY, Guérard F, Montavon G, Galland N. In vivo stability of 211At-radiopharmaceuticals: on the impact of halogen bond formation. RSC Med Chem 2024; 15:223-233. [PMID: 38283213 PMCID: PMC10809332 DOI: 10.1039/d3md00579h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 01/30/2024] Open
Abstract
211At, when coupled to a targeting agent, is one of the most promising radionuclides for therapeutic applications. The main labelling approach consists in the formation of astatoaryl compounds, which often show a lack of in vivo stability. The hypothesis that halogen bond (XB) interactions with protein functional groups initiate a deastatination mechanism is investigated through radiochemical experiments and DFT modelling. Several descriptors agree on the known mechanism of iodoaryl substrates dehalogenation by iodothyronine deiodinases, supporting the higher in vivo dehalogenation of N-succinimidyl 3-[211At]astatobenzoate (SAB) conjugates in comparison with their iodinated counterparts. The guanidinium group in 3-[211At]astato-4-guanidinomethylbenzoate (SAGMB) prevents the formation of At-mediated XBs with the selenocysteine active site in iodothyronine deiodinases. The initial step of At-aryl bond dissociation is inhibited, elucidating the better in vivo stability of SAGMB conjugates compared with those of SAB. The impact of astatine's ability to form XB interactions on radiopharmaceutical degradation may not be limited to the case of aryl radiolabeling.
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Affiliation(s)
- Thibault Yssartier
- CNRS, CEISAM UMR 6230, Nantes Université F-44000 Nantes France
- CNRS, SUBATECH UMR 6457, IMT Atlantique F-44307 Nantes France
| | - Lu Liu
- CNRS, IPHC UMR 7178, Université de Strasbourg F-67037 Strasbourg France
| | - Sylvain Pardoue
- CNRS, SUBATECH UMR 6457, IMT Atlantique F-44307 Nantes France
| | | | - François Guérard
- Inserm UMR 1307, CNRS UMR 6075, CRCI2NA, Nantes Université, Université d'Angers F-44000 Nantes France
| | - Gilles Montavon
- CNRS, SUBATECH UMR 6457, IMT Atlantique F-44307 Nantes France
| | - Nicolas Galland
- CNRS, CEISAM UMR 6230, Nantes Université F-44000 Nantes France
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15
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Witoszka K, Matalińska J, Misicka A, Lipiński PFJ. Moving out of CF 3 -Land: Synthesis, Receptor Affinity, and in silico Studies of NK1 Receptor Ligands Containing a Pentafluorosulfanyl (SF 5 ) Group. ChemMedChem 2023; 18:e202300315. [PMID: 37821725 DOI: 10.1002/cmdc.202300315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023]
Abstract
The NK1 receptor (NK1R) is a molecular target for both approved and experimental drugs intended for a variety of conditions, including emesis, pain, and cancers. While contemplating modifications to the typical NK1R pharmacophore, we wondered whether the CF3 groups common for many NK1R ligands, could be replaced with some other moiety. Our attention was drawn by the SF5 group, and so we designed, synthesized, and tested ten novel SF5 -containing compounds for NK1R affinity. All analogues exhibit detectable NK1R binding, with the best of them, compound 5 a, (3-bromo-5-(pentafluoro-λ6 -sulfanyl)benzyl acetyl-L-tryptophanate) binding only slightly worse (IC50 =34.3 nM) than the approved NK1R-targeting drug, aprepitant (IC50 =27.7 nM). Molecular docking provided structural explanation of SAR. According to our analysis, the SF5 group in our compounds occupies a position similar to that of one of the CF3 groups of aprepitant as found in the crystal structure. Additionally, we checked whether the docking scoring function or energies derived from Fragment Molecular Orbital quantum chemical calculations may be helpful in explaining and predicting the experimental receptor affinities for our analogues. Both these methods produce moderately good results. Overall, this is the first demonstration of the utility of the SF5 group in the design of NK1R ligands.
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Affiliation(s)
- Katarzyna Witoszka
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
| | - Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
| | - Aleksandra Misicka
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
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16
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Schuurs ZP, Martyn AP, Soltau CP, Beard S, Shah ET, Adams MN, Croft LV, O’Byrne KJ, Richard DJ, Gandhi NS. An Exploration of Small Molecules That Bind Human Single-Stranded DNA Binding Protein 1. BIOLOGY 2023; 12:1405. [PMID: 37998004 PMCID: PMC10669474 DOI: 10.3390/biology12111405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/25/2023]
Abstract
Human single-stranded DNA binding protein 1 (hSSB1) is critical to preserving genome stability, interacting with single-stranded DNA (ssDNA) through an oligonucleotide/oligosaccharide binding-fold. The depletion of hSSB1 in cell-line models leads to aberrant DNA repair and increased sensitivity to irradiation. hSSB1 is over-expressed in several types of cancers, suggesting that hSSB1 could be a novel therapeutic target in malignant disease. hSSB1 binding studies have focused on DNA; however, despite the availability of 3D structures, small molecules targeting hSSB1 have not been explored. Quinoline derivatives targeting hSSB1 were designed through a virtual fragment-based screening process, synthesizing them using AlphaLISA and EMSA to determine their affinity for hSSB1. In parallel, we further screened a structurally diverse compound library against hSSB1 using the same biochemical assays. Three compounds with nanomolar affinity for hSSB1 were identified, exhibiting cytotoxicity in an osteosarcoma cell line. To our knowledge, this is the first study to identify small molecules that modulate hSSB1 activity. Molecular dynamics simulations indicated that three of the compounds that were tested bound to the ssDNA-binding site of hSSB1, providing a framework for the further elucidation of inhibition mechanisms. These data suggest that small molecules can disrupt the interaction between hSSB1 and ssDNA, and may also affect the ability of cells to repair DNA damage. This test study of small molecules holds the potential to provide insights into fundamental biochemical questions regarding the OB-fold.
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Affiliation(s)
- Zachariah P. Schuurs
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia; (Z.P.S.); (A.P.M.)
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
| | - Alexander P. Martyn
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia; (Z.P.S.); (A.P.M.)
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
| | - Carl P. Soltau
- School of Chemistry and Physics, Centre for Materials Science, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Sam Beard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
| | - Esha T. Shah
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Mark N. Adams
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Laura V. Croft
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Kenneth J. O’Byrne
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
- Cancer Services, Princess Alexandra Hospital—Metro South Health, Woolloongabba, QLD 4102, Australia
| | - Derek J. Richard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Neha S. Gandhi
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia; (Z.P.S.); (A.P.M.)
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Woolloongabba, QLD 4102, Australia; (S.B.); (M.N.A.); (L.V.C.); (K.J.O.); (D.J.R.)
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, India
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17
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Serna-Arbeláez MS, García-Cárcamo V, Rincón-Tabares DS, Guerra D, Loaiza-Cano V, Martinez-Gutierrez M, Pereañez JA, Pastrana-Restrepo M, Galeano E, Zapata W. In Vitro and In Silico Antiviral Activity of Di-Halogenated Compounds Derived from L-Tyrosine against Human Immunodeficiency Virus 1 (HIV-1). Curr Issues Mol Biol 2023; 45:8173-8200. [PMID: 37886959 PMCID: PMC10605077 DOI: 10.3390/cimb45100516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
HIV-1 infection is considered one of the major public health problems worldwide. Due to the limited access to antiretroviral therapy, the associated side effects, and the resistance that the virus can generate, it has become necessary to continue the development of new antiviral agents. The study aimed to identify potential antiviral agents for HIV-1 by evaluating the in vitro and in silico activity of 16 synthetic di-halogenated compounds derived from L-Tyrosine. The compounds were tested for cytotoxicity, which was determined using MTT, and a combined antiviral screening strategy (pre- and post-infection treatment) was performed against R5 and X4 strains of HIV-1. The most promising compounds were evaluated against a pseudotyped virus (HIV-GFP-VSV-G), and the effectiveness of these compounds was measured through GFP flow cytometry. Also, the antiviral effect of these compounds was evaluated in PBMCs using flow cytometry and ELISA for p24. The TODB-2M, TODC-2M, TODC-3M, and YDC-3M compounds showed low toxicity and significant inhibitory activity against HIV-1. In silico docking and molecular dynamics assays suggest that the compounds' antiviral activity may be due to interaction with reverse transcriptase, viral protease, or envelope gp120.
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Affiliation(s)
- Maria S. Serna-Arbeláez
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín 050001, Colombia; (M.S.S.-A.); (V.G.-C.)
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín 050001, Colombia;
| | - Valentina García-Cárcamo
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín 050001, Colombia; (M.S.S.-A.); (V.G.-C.)
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín 050001, Colombia;
| | - Daniel S. Rincón-Tabares
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín 050001, Colombia;
| | - Diego Guerra
- Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas, PTS Granada, 18016 Granada, Spain;
- Programa de Estudio y Control de Enfermedades Tropicales PECET, Faculty of Medicine, University of Antioquia, Medellín 050010, Colombia
| | - Vanessa Loaiza-Cano
- Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680005, Colombia; (V.L.-C.); (M.M.-G.)
| | - Marlen Martinez-Gutierrez
- Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680005, Colombia; (V.L.-C.); (M.M.-G.)
| | - Jaime A. Pereañez
- Grupo Toxinología, Alternativas Terapéuticas y Alimentarias, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Medellín 050001, Colombia;
| | - Manuel Pastrana-Restrepo
- Productos Naturales Marinos, Departamento de Farmacia, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Medellín 050001, Colombia; (M.P.-R.); (E.G.)
| | - Elkin Galeano
- Productos Naturales Marinos, Departamento de Farmacia, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Medellín 050001, Colombia; (M.P.-R.); (E.G.)
| | - Wildeman Zapata
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín 050001, Colombia; (M.S.S.-A.); (V.G.-C.)
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín 050001, Colombia;
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18
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Hernández-Ruiz R, Gómez-Gil S, Pedrosa MR, Suárez-Pantiga S, Sanz R. Direct synthesis of haloaromatics from nitroarenes via a sequential one-pot Mo-catalyzed reduction/Sandmeyer reaction. Org Biomol Chem 2023; 21:7791-7798. [PMID: 37706648 DOI: 10.1039/d3ob01187a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Herein, we report the direct synthesis of a wide variety of functionalized aromatic bromides, chlorides, iodides, and fluorides from nitroarenes in a sequential one-pot operation. This protocol is based on an air- and moisture-tolerant dioxomolybdenum-catalyzed reduction of nitroaromatics, employing pinacol as a reducing agent, which enables subsequent diazotization and halogenation steps. This methodology represents a step-economical, practical, and alternative procedure for synthesizing haloaromatics directly from nitroaromatics.
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Affiliation(s)
- Raquel Hernández-Ruiz
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain.
| | - Sara Gómez-Gil
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain.
| | - María R Pedrosa
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain.
| | - Samuel Suárez-Pantiga
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain.
| | - Roberto Sanz
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain.
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19
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Guo C, Li Q, Xiao J, Ma F, Xia X, Shi M. Identification of defactinib derivatives targeting focal adhesion kinase using ensemble docking, molecular dynamics simulations and binding free energy calculations. J Biomol Struct Dyn 2023; 41:8654-8670. [PMID: 36281703 DOI: 10.1080/07391102.2022.2135601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/08/2022] [Indexed: 10/31/2022]
Abstract
Focal adhesion kinase (FAK) belongs to the nonreceptor tyrosine kinases, which selectively phosphorylate tyrosine residues on substrate proteins. FAK is associated with bladder, esophageal, gastric, neck, breast, ovarian and lung cancers. Thus, FAK has been considered as a potential target for tumor treatment. Currently, there are six adenosine triphosphate (ATP)-competitive FAK inhibitors tested in clinical trials but no approved inhibitors targeting FAK. Defactinib (VS-6063) is a second-generation FAK inhibitor with an IC50 of 0.6 nM. The binding model of VS-6063 with FAK may provide a reference model for developing new antitumor FAK-targeting drugs. In this study, the VS-6063/FAK binding model was constructed using ensemble docking and molecular dynamics simulations. Furthermore, the molecular mechanics/generalized Born (GB) surface area (MM/GBSA) method was employed to estimate the binding free energy between VS-6063 and FAK. The key residues involved in VS-6063/FAK binding were also determined using per-residue energy decomposition analysis. Based on the binding model, VS-6063 could be separated into seven regions to enhance its binding affinity with FAK. Meanwhile, 60 novel defactinib-based compounds were designed and verified using ensemble docking. Overall, the present study improves our understanding of the binding mechanism of human FAK with VS-6063 and provides new insights into future drug designs targeting FAK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chuan Guo
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Qinxuan Li
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Jiujia Xiao
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Feng Ma
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Xun Xia
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Mingsong Shi
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
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20
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Durai P, Lee SJ, Lee JW, Pan CH, Park K. Iterative machine learning-based chemical similarity search to identify novel chemical inhibitors. J Cheminform 2023; 15:86. [PMID: 37742003 PMCID: PMC10517535 DOI: 10.1186/s13321-023-00760-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
Machine learning-based chemical screening has made substantial progress in recent years. However, these predictions often have low accuracy and high uncertainty when identifying new active chemical scaffolds. Hence, a high proportion of retrieved compounds are not structurally novel. In this study, we proposed a strategy to address this issue by iteratively optimizing an evolutionary chemical binding similarity (ECBS) model using experimental validation data. Various data update and model retraining schemes were tested to efficiently incorporate new experimental data into ECBS models, resulting in a fine-tuned ECBS model with improved accuracy and coverage. To demonstrate the effectiveness of our approach, we identified the novel hit molecules for the mitogen-activated protein kinase kinase 1 (MEK1). These molecules showed sub-micromolar affinity (Kd 0.1-5.3 μM) to MEKs and were distinct from previously-known MEK1 inhibitors. We also determined the binding specificity of different MEK isoforms and proposed potential docking models. Furthermore, using de novo drug design tools, we utilized one of the new MEK inhibitors to generate additional drug-like molecules with improved binding scores. This resulted in the identification of several potential MEK1 inhibitors with better binding affinity scores. Our results demonstrated the potential of this approach for identifying novel hit molecules and optimizing their binding affinities.
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Affiliation(s)
- Prasannavenkatesh Durai
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Sue Jung Lee
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Jae Wook Lee
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Cheol-Ho Pan
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea.
- Department of YM-KIST Bio-Health Convergence, Yonsei University, Wonju, 26493, Republic of Korea.
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21
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West AML, Dominelli‐Whiteley N, Smolyar IV, Nichol GS, Cockroft SL. Experimental Quantification of Halogen⋅⋅⋅Arene van der Waals Contacts. Angew Chem Int Ed Engl 2023; 62:e202309682. [PMID: 37470309 PMCID: PMC10953438 DOI: 10.1002/anie.202309682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Crystallographic and computational studies suggest the occurrence of favourable interactions between polarizable arenes and halogen atoms. However, the systematic experimental quantification of halogen⋅⋅⋅arene interactions in solution has been hindered by the large variance in the steric demands of the halogens. Here we have synthesized molecular balances to quantify halogen⋅⋅⋅arene contacts in 17 solvents and solvent mixtures using 1 H NMR spectroscopy. Calculations indicate that favourable halogen⋅⋅⋅arene interactions arise from London dispersion in the gas phase. In contrast, comparison of our experimental measurements with partitioned SAPT0 energies indicate that dispersion is sufficiently attenuated by the solvent that the halogen⋅⋅⋅arene interaction trend was instead aligned with increasing exchange repulsion as the halogen increased in size (ΔGX ⋅⋅⋅Ph =0 to +1.5 kJ mol-1 ). Halogen⋅⋅⋅arene contacts were slightly less disfavoured in solvents with higher solvophobicities and lower polarizabilities, but strikingly, were always less favoured than CH3 ⋅⋅⋅arene contacts (ΔGMe ⋅⋅⋅Ph =0 to -1.4 kJ mol-1 ).
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Affiliation(s)
- Andrew M. L. West
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Nicholas Dominelli‐Whiteley
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Ivan V. Smolyar
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Gary S. Nichol
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Scott L. Cockroft
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
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22
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Keuper AC, Fengler K, Ostler F, Danelzik T, Piekarski DG, García Mancheño O. Fine-Tuning Substrate-Catalyst Halogen-Halogen Interactions for Boosting Enantioselectivity in Halogen-Bonding Catalysis. Angew Chem Int Ed Engl 2023; 62:e202304781. [PMID: 37228095 DOI: 10.1002/anie.202304781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/08/2023] [Accepted: 05/25/2023] [Indexed: 05/27/2023]
Abstract
A new approach towards highly enantioselective halogen-bonding catalysis has been developed. To circumvent the intrinsic issues of the nature of the halogen-bond (XB) and the resultant unresolved limitations in asymmetric catalysis, fine-tuned halogen-halogen interactions between the substrate and XB-donor were designed to preorganize the substrate in the catalyst's cavity and boost enantiocontrol. The present strategy exploits both the electron cloud (Lewis base site) and the sigma (σ)-hole site of the halogen substituent of the substrates to form a tight catalyst-substrate-counteranion chiral complex, thus enabling a controlled induction of high levels of chirality transfer. Remarkable enantioselectivities of up to 95 : 5 e.r. (90 % ee) have been achieved in a model dearomatization reaction of halogen-substituted (iso)quinolines with tetrakis-iodotriazole multidentate anion-binding catalysts.
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Affiliation(s)
- Alica C Keuper
- Organic Chemistry Institute, University of Münster, Correnstraße 36/40, 48149, Münster, Germany
| | - Kevin Fengler
- Organic Chemistry Institute, University of Münster, Correnstraße 36/40, 48149, Münster, Germany
| | - Florian Ostler
- Organic Chemistry Institute, University of Münster, Correnstraße 36/40, 48149, Münster, Germany
| | - Tobias Danelzik
- Organic Chemistry Institute, University of Münster, Correnstraße 36/40, 48149, Münster, Germany
| | - Dariusz G Piekarski
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Poland
| | - Olga García Mancheño
- Organic Chemistry Institute, University of Münster, Correnstraße 36/40, 48149, Münster, Germany
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23
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Piña MDLN, Bauzá A. On the Importance of Halogen and Chalcogen Bonds in the Solid State of Nucleic Acids: A Combined Crystallographic and Theoretical Perspective. Int J Mol Sci 2023; 24:13035. [PMID: 37685843 PMCID: PMC10488009 DOI: 10.3390/ijms241713035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/16/2023] [Accepted: 08/20/2023] [Indexed: 09/10/2023] Open
Abstract
In this work, intra- and intermolecular halogen and chalcogen bonds (HlgBs and ChBs, respectively) present in the solid state of nucleic acids (NAs) have been studied at the RI-MP2/def2-TZVP level of theory. To achieve this, a Protein Data Bank (PDB) survey was carried out, revealing a series of structures in which Br/I or S/Se/Te atoms belonging to nucleobases or pentose rings were involved in noncovalent interactions (NCIs) with electron-rich species. The energetics and directionality of these NCIs were rationalized through a computational study, which included the use of Molecular Electrostatic Potential (MEP) surfaces, the Quantum Theory of Atoms in Molecules (QTAIM), and Non Covalent Interaction plot (NCIplot) and Natural Bonding Orbital (NBO) techniques.
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Affiliation(s)
| | - Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa Km 7.5, 07122 Palma de Mallorca, Baleares, Spain;
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24
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Grineva OV. Comparison of Intermolecular Halogen...Halogen Distances in Organic and Organometallic Crystals. Int J Mol Sci 2023; 24:11911. [PMID: 37569289 PMCID: PMC10419058 DOI: 10.3390/ijms241511911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/15/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Statistical analysis of halogen...halogen intermolecular distances was performed for three sets of homomolecular crystals under normal conditions: C-Hal1...Hal2-C distances in crystals consisting of: (i) organic compounds (set Org); (ii) organometallic compounds (set Orgmet); and (iii) distances M1-Hal1...Hal2-M2 (set MHal) (in all cases Hal1 = Hal2, and in MHal M1 = M2, M is any metal). When analyzing C-Hal...Hal-C distances, a new method for estimating the values of van der Waals radii is proposed, based on the use of two subsets of distances: (i) the shortest distances from each substance less than a threshold; and (ii) all C-Hal...Hal-C distances less than the same threshold. As initial approximations for these thresholds for different Hal, the Ragg values previously introduced in investigations with the participation of the author were used (Ragg values make it possible to perform a statistical assessment of the presence of halogen aggregates in crystals). The following values are recommended in this work to be used as universal values for crystals of organic and organometallic compounds: RF = 1.57, RCl = 1.90, RBr = 1.99, and RI = 2.15 Å. They are in excellent agreement with the results of some other works but significantly (by 0.10-0.17 Å) greater than the commonly used values. For the Orgmet set, slightly lower values for RI (2.11-2.09 Å) were obtained, but number of the C-I...I-C distances available for analysis was significantly smaller than in the other subgroups, which may be the reason for the discrepancy with value for the Org set (2.15 Å). Statistical analysis of the M-Hal...Hal-M distances was performed for the first time. A Hal-aggregation coefficient for M-Hal bonds is proposed, which allows one to estimate the propensity of M-Hal groups with certain M and Hal to participate in Hal-aggregates formed by M-Hal...Hal-M contacts. In particular, it was found that, for the Hg-Hal groups (Hal = Cl, Br, I), there is a high probability that the crystals have Hg-Hal...Hal-Hg distances with length ≤ Ragg.
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Affiliation(s)
- Olga V Grineva
- Chemistry Department, Moscow M. V. Lomonosov State University, 119991 Moscow, Russia
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25
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Adhav V, Saikrishnan K. The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function. ACS OMEGA 2023; 8:22268-22284. [PMID: 37396257 PMCID: PMC10308531 DOI: 10.1021/acsomega.3c00205] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.
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26
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Mizuguchi M, Yokoyama T, Okada T, Nakagawa Y, Fujii K, Nabeshima Y, Toyooka N. Benziodarone and 6-hydroxybenziodarone are potent and selective inhibitors of transthyretin amyloidogenesis. Bioorg Med Chem 2023; 90:117370. [PMID: 37311373 DOI: 10.1016/j.bmc.2023.117370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
Transthyretin amyloidosis is a progressive systemic disorder that is caused by the amyloid deposition of transthyretin in various organs. Stabilization of the native transthyretin is an effective strategy for the treatment of transthyretin amyloidosis. In this study we demonstrate that the clinically used uricosuric agent benziodarone is highly effective to stabilize the tetrameric structure of transthyretin. An acid-induced aggregation assay showed that benziodarone had strong inhibitory activity similar to that of tafamidis, which is currently used as a therapeutic agent for transthyretin amyloidosis. Moreover, a possible metabolite, 6-hydroxybenziodarone, retained the strong amyloid inhibitory activity of benziodarone. An ex vivo competitive binding assay using a fluorogenic probe showed that benziodarone and 6-hydroxybenziodarone were highly potent for selective binding to transthyretin in human plasma. An X-ray crystal structure analysis revealed that the halogenated hydroxyphenyl ring was located at the entrance of the thyroxine binding channel of transthyretin and that the benzofuran ring was located in the inner channel. These studies suggest that benziodarone and 6-hydroxybenziodarone would potentially be effective against transthyretin amyloidosis.
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Affiliation(s)
- Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan.
| | - Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Takuya Okada
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan; Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Japan
| | - Yusuke Nakagawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Japan
| | - Kanako Fujii
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Naoki Toyooka
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan; Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Japan
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27
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Chiodi D, Ishihara Y. "Magic Chloro": Profound Effects of the Chlorine Atom in Drug Discovery. J Med Chem 2023; 66:5305-5331. [PMID: 37014977 DOI: 10.1021/acs.jmedchem.2c02015] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Chlorine is one of the most common atoms present in small-molecule drugs beyond carbon, hydrogen, nitrogen, and oxygen. There are currently more than 250 FDA-approved chlorine-containing drugs, yet the beneficial effect of the chloro substituent has not yet been reviewed. The seemingly simple substitution of a hydrogen atom (R = H) with a chlorine atom (R = Cl) can result in remarkable improvements in potency of up to 100,000-fold and can lead to profound effects on pharmacokinetic parameters including clearance, half-life, and drug exposure in vivo. Following the literature terminology of the "magic methyl effect" in drugs, the term "magic chloro effect" has been coined herein. Although reports of 500-fold or 1000-fold potency improvements are often serendipitous discoveries that can be considered "magical" rather than planned, hypotheses made to explain the magic chloro effect can lead to lessons that accelerate the cycle of drug discovery.
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Affiliation(s)
- Debora Chiodi
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yoshihiro Ishihara
- Department of Chemistry, Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, California 92121, United States
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28
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Pandey KP, Divović B, Rashid F, Golani LK, Cerne R, Zahn NM, Meyer MJ, Arnold LA, Sharmin D, Mian MY, Smith JL, Ping X, Jin X, Lippa A, Tiruveedhula VVNPB, Cook JM, Savić MM, Witkin JM. Structural Analogs of the GABAkine KRM-II-81 Are Orally Bioavailable Anticonvulsants without Sedation. J Pharmacol Exp Ther 2023; 385:50-61. [PMID: 36746611 PMCID: PMC10029819 DOI: 10.1124/jpet.122.001362] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 12/22/2022] [Accepted: 01/19/2023] [Indexed: 02/08/2023] Open
Abstract
To provide back-up compounds to support the development of the GABAA receptor (GABAAR) potentiator KRM-II-81, three novel analogs were designed: replacing the pyridinyl with 2'-Cl-phenyl (FR-II-60), changing the positions of the N and O atoms in the oxazole ring with addition of an ethyl group (KPP-III-34 and KPP-III-51), or substituting a Br atom for the ethynyl of KRM-II-81 (KPP-III-34). The compounds bound to brain GABAARs. Intraperitoneal administration of FR-II-60 and KPP-III-34 produced anticonvulsant activity in mice [maximal electroshock (MES)-induced seizures or 6 Hz-induced seizures], whereas KPP-III-51 did not. Although all compounds were orally bioavailable, structural changes reduced the plasma and brain (FR-II-60 and KPP-III-51) exposures relative to KRM-II-81. Oral administration of each compound produced dose-dependent increases in the latency for both clonic and tonic seizures and the lethality induced by pentylenetetrazol (PTZ) in mice. Since KPP-III-34 produced the highest brain area under the curve (AUC) exposures, it was selected for further profiling. Oral administration of KPP-III-34 suppressed seizures in corneal-kindled mice, hippocampal paroxysmal discharges in mesial temporal lobe epileptic mice, and PTZ-induced convulsions in rats. Only transient sensorimotor impairment was observed in mice, and doses of KPP-III-34 up to 500 mg/kg did not produce impairment in rats. Molecular docking studies demonstrated that all compounds displayed a reduced propensity for binding to α1His102 compared with the sedating compound alprazolam; the bromine-substituted KPP-III-34 achieved the least interaction. Overall, these findings document the oral bioavailability and anticonvulsant efficacy of three novel analogs of KRM-II-81 with reduced sedative effects. SIGNIFICANCE STATEMENT: A new non-sedating compound, KRM-II-81, with reduced propensity for tolerance is moving into clinical development. Three new analogs were orally bioavailable, produced anticonvulsant effects in rodents, and displayed low sensorimotor impairment. KPP-III-34 demonstrated efficacy in models of pharmacoresistant epilepsy. Docking studies demonstrated a low propensity for compound binding to the α1His102 residue implicated in sedation. Thus, three additional structures have been added to the list of non-sedating imidazodiazepine anticonvulsants that could serve as backups in the clinical development of KRM-II-81.
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Affiliation(s)
- Kamal P Pandey
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.);
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.);
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.);
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.);
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Branka Divović
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Farjana Rashid
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Lalit K Golani
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Rok Cerne
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Nicolas M Zahn
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Michelle Jean Meyer
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Leggy A Arnold
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Dishary Sharmin
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Md Yeunus Mian
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Jodi L Smith
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Xingjie Ping
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Xiaoming Jin
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Arnold Lippa
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - V V N Phani Babu Tiruveedhula
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - James M Cook
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Miroslav M Savić
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.)
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.)
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.)
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.)
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
| | - Jeffrey M Witkin
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin (K.P.P., F.R., L.K.G., N.M.Z., M.J.M., L.A.A., D.S., M.Y.M., V.V.N.P.B.T., J.M.C., J.M.W.);
- Department of Pharmacology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia (B.D., M.M.S.);
- Laboratory of Antiepileptic Drug Discovery, St. Vincent's Hospital, Indianapolis, Indiana (R.C., J.L.S., J.M.W.);
- Department of Anatomy and Cell BiologyIndiana University/Purdue University, Indianapolis, Indiana (R.C., X.P., X.J.);
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia (R.C.); and RespireRx Pharmaceuticals Inc., Glen Rock, New Jersey (A.L., J.M.C., J.M.W.)
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Chen Y, Zhuo M, Wen X, Chen W, Zhang K, Li M. Organic Photothermal Cocrystals: Rational Design, Controlled Synthesis, and Advanced Application. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206830. [PMID: 36707495 PMCID: PMC10104673 DOI: 10.1002/advs.202206830] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/22/2022] [Indexed: 05/22/2023]
Abstract
Organic photothermal cocrystals, integrating the advantages of intrinsic organic cocrystals and the fascinating photothermal conversion ability, hold attracted considerable interest in both basic science and practical applications, involving photoacoustic imaging, seawater desalination, and photothermal therapy, and so on. However, these organic photothermal cocrystals currently suffer individual cases discovered step by step, as well as the deep and systemic investigation in the corresponding photothermal conversion mechanisms is rarely carried out, suggesting a huge challenge for their further developments. Therefore, it is urgently necessary to investigate and explore the rational design and synthesis of high-performance organic photothermal cocrystals for future applications. This review first and systematically summarizes the organic photothermal cocrystal in terms of molecular classification, the photothermal conversion mechanism, and their corresponding applications. The timely interpretation of the cocrystal photothermal effect will provide broad prospects for the purposeful fabrication of excellent organic photothermal cocrystals toward great efficiency, low cost, and multifunctionality.
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Affiliation(s)
- Ye‐Tao Chen
- College of Chemistry and Chemical Engineering and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong ProvinceShantou University515063ShantouChina
| | - Ming‐Peng Zhuo
- National Engineering Laboratory for Modern SilkCollege of Textile and Clothing EngineeringSoochow UniversitySuzhou215123China
| | - Xinyi Wen
- College of Chemistry and Chemical Engineering and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong ProvinceShantou University515063ShantouChina
| | - Wenbin Chen
- College of Chemistry and Chemical Engineering and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong ProvinceShantou University515063ShantouChina
| | - Ke‐Qin Zhang
- National Engineering Laboratory for Modern SilkCollege of Textile and Clothing EngineeringSoochow UniversitySuzhou215123China
| | - Ming‐De Li
- College of Chemistry and Chemical Engineering and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong ProvinceShantou University515063ShantouChina
- Chemistry and Chemical Engineering Guangdong LaboratoryShantou UniversityShantou515031China
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30
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Tököli A, Bodnár B, Bogár F, Paragi G, Hetényi A, Bartus É, Wéber E, Hegedüs Z, Szabó Z, Kecskeméti G, Szakonyi G, Martinek TA. Structural Adaptation of the Single-Stranded DNA-Binding Protein C-Terminal to DNA Metabolizing Partners Guides Inhibitor Design. Pharmaceutics 2023; 15:pharmaceutics15041032. [PMID: 37111518 PMCID: PMC10143822 DOI: 10.3390/pharmaceutics15041032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Single-stranded DNA-binding protein (SSB) is a bacterial interaction hub and an appealing target for antimicrobial therapy. Understanding the structural adaptation of the disordered SSB C-terminus (SSB-Ct) to DNA metabolizing enzymes (e.g., ExoI and RecO) is essential for designing high-affinity SSB mimetic inhibitors. Molecular dynamics simulations revealed the transient interactions of SSB-Ct with two hot spots on ExoI and RecO. The residual flexibility of the peptide-protein complexes allows adaptive molecular recognition. Scanning with non-canonical amino acids revealed that modifications at both termini of SSB-Ct could increase the affinity, supporting the two-hot-spot binding model. Combining unnatural amino acid substitutions on both segments of the peptide resulted in enthalpy-enhanced affinity, accompanied by enthalpy-entropy compensation, as determined by isothermal calorimetry. NMR data and molecular modeling confirmed the reduced flexibility of the improved affinity complexes. Our results highlight that the SSB-Ct mimetics bind to the DNA metabolizing targets through the hot spots, interacting with both of segments of the ligands.
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Affiliation(s)
- Attila Tököli
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Brigitta Bodnár
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
| | - Ferenc Bogár
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
| | - Gábor Paragi
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- Institute of Physics, University of Pécs, H7624 Pécs, Hungary
- Department of Theoretical Physics, University of Szeged, H6720 Szeged, Hungary
| | - Anasztázia Hetényi
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Éva Bartus
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
| | - Edit Wéber
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Zoltán Szabó
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Gábor Kecskeméti
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Gerda Szakonyi
- Institute of Pharmaceutical Analysis, University of Szeged, H6720 Szeged, Hungary
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
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31
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A Comprehensive Ab Initio Study of Halogenated A···U and G···C Base Pair Geometries and Energies. Int J Mol Sci 2023; 24:ijms24065530. [PMID: 36982603 PMCID: PMC10056977 DOI: 10.3390/ijms24065530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/09/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023] Open
Abstract
Unraveling the binding preferences involved in the formation of a supramolecular complex is key to properly understand molecular recognition and aggregation phenomena, which are of pivotal importance to biology. The halogenation of nucleic acids has been routinely carried out for decades to assist in their X-ray diffraction analysis. The incorporation of a halogen atom on a DNA/RNA base not only affected its electronic distribution, but also expanded the noncovalent interactions toolbox beyond the classical hydrogen bond (HB) by incorporating the halogen bond (HalB). In this regard, an inspection of the Protein Data Bank (PDB) revealed 187 structures involving halogenated nucleic acids (either unbound or bound to a protein) where at least 1 base pair (BP) exhibited halogenation. Herein, we were interested in disclosing the strength and binding preferences of halogenated A···U and G···C BPs, which are predominant in halogenated nucleic acids. To achieve that, computations at the RI-MP2/def2-TZVP level of theory together with state of the art theoretical modeling tools (including the computation of molecular electrostatic potential (MEP) surfaces, the quantum theory of “Atoms in Molecules” (QTAIM) and the non-covalent interactions plot (NCIplot) analyses) allowed for the characterization of the HB and HalB complexes studied herein.
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32
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Ding Y, Chen S, Zhang F, Li W, Ge G, Liu T, Yang Q. Chitinase is a Potent Insecticidal Molecular Target of Camptothecin and Its Derivatives. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1845-1851. [PMID: 36655791 DOI: 10.1021/acs.jafc.2c06607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Camptothecin (CPT) is a prominent molecule in natural product research because of its application prospects in medicine and agriculture. In this study, CPT and its derivatives were discovered to be competitive inhibitors of group II and group h insect chitinases, both of which are key components of insect chitinolytic systems. CPT and 7-ethyl-10-hydroxycamptothecin (SN-38) inhibited group II chitinase from Ostrinia furnacalis (OfChtII) with Ki values of 5.1 and 2.0 μM, respectively. Results from tryptophan fluorescence spectroscopy, molecular docking analysis, and molecular dynamics simulations revealed that both CPT and SN-38 inhibit OfChtII-C1 by interacting with solvent-exposed tryptophan residues in a substrate-binding cleft. CPT exhibited high insecticidal activity toward the orthopteran pest Locusta migratoria, possibly because of the midgut metabolism of CPT, with only moderate activities toward lepidopteran pests. Even though SN-38 exhibited much lower insecticidal activities than CPT, it still showed higher inhibitory activity toward chitinase. This study reports a new molecular target of CPT and provides insights into molecular design of CPT-based insecticides against different kinds of pests.
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Affiliation(s)
- Yi Ding
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Sizhe Chen
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Feng Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wenda Li
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Tian Liu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Qing Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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33
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Wang D, Wu Z, Shen C, Bao L, Luo H, Wang Z, Yao H, Kong DX, Luo C, Hou T. Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors. Brief Bioinform 2023; 24:6961473. [PMID: 36573494 DOI: 10.1093/bib/bbac592] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
Machine learning including modern deep learning models has been extensively used in drug design and screening. However, reliable prediction of molecular properties is still challenging when exploring out-of-domain regimes, even for deep neural networks. Therefore, it is important to understand the uncertainty of model predictions, especially when the predictions are used to guide further experiments. In this study, we explored the utility and effectiveness of evidential uncertainty in compound screening. The evidential Graphormer model was proposed for uncertainty-guided discovery of KDM1A/LSD1 inhibitors. The benchmarking results illustrated that (i) Graphormer exhibited comparative predictive power to state-of-the-art models, and (ii) evidential regression enabled well-ranked uncertainty estimates and calibrated predictions. Subsequently, we leveraged time-splitting on the curated KDM1A/LSD1 dataset to simulate out-of-distribution predictions. The retrospective virtual screening showed that the evidential uncertainties helped reduce false positives among the top-acquired compounds and thus enabled higher experimental validation rates. The trained model was then used to virtually screen an independent in-house compound set. The top 50 compounds ranked by two different ranking strategies were experimentally validated, respectively. In general, our study highlighted the importance to understand the uncertainty in prediction, which can be recognized as an interpretable dimension to model predictions.
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Affiliation(s)
- Dong Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou 310058 Zhejiang, China
| | - Zhenxing Wu
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou 310058 Zhejiang, China
| | - Chao Shen
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou 310058 Zhejiang, China.,CarbonSilicon AI Technology Co., Ltd, Hangzhou 310018, Zhejiang, China
| | - Lingjie Bao
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou 310058 Zhejiang, China
| | - Hao Luo
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou 310058 Zhejiang, China
| | - Zhe Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou 310058 Zhejiang, China
| | - Hucheng Yao
- State Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - De-Xin Kong
- State Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Luo
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203 China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou 310058 Zhejiang, China
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34
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Pinel P, Guichaoua G, Najm M, Labouille S, Drizard N, Gaston-Mathé Y, Hoffmann B, Stoven V. Exploring isofunctional molecules: Design of a benchmark and evaluation of prediction performance. Mol Inform 2023; 42:e2200216. [PMID: 36633361 DOI: 10.1002/minf.202200216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/19/2022] [Accepted: 01/11/2023] [Indexed: 01/13/2023]
Abstract
Identification of novel chemotypes with biological activity similar to a known active molecule is an important challenge in drug discovery called 'scaffold hopping'. Small-, medium-, and large-step scaffold hopping efforts may lead to increasing degrees of chemical structure novelty with respect to the parent compound. In the present paper, we focus on the problem of large-step scaffold hopping. We assembled a high quality and well characterized dataset of scaffold hopping examples comprising pairs of active molecules and including a variety of protein targets. This dataset was used to build a benchmark corresponding to the setting of real-life applications: one active molecule is known, and the second active is searched among a set of decoys chosen in a way to avoid statistical bias. This allowed us to evaluate the performance of computational methods for solving large-step scaffold hopping problems. In particular, we assessed how difficult these problems are, particularly for classical 2D and 3D ligand-based methods. We also showed that a machine-learning chemogenomic algorithm outperforms classical methods and we provided some useful hints for future improvements.
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Affiliation(s)
- Philippe Pinel
- Center for Computational Biology, Mines Paris-PSL, PSL Research University, 75006, Paris, France.,Institut Curie, 75248, Paris, France.,INSERM U900, 75428, Paris, France.,Iktos SAS, 75017, Paris, France
| | - Gwenn Guichaoua
- Center for Computational Biology, Mines Paris-PSL, PSL Research University, 75006, Paris, France.,Institut Curie, 75248, Paris, France.,INSERM U900, 75428, Paris, France
| | - Matthieu Najm
- Center for Computational Biology, Mines Paris-PSL, PSL Research University, 75006, Paris, France.,Institut Curie, 75248, Paris, France.,INSERM U900, 75428, Paris, France
| | | | | | | | | | - Véronique Stoven
- Center for Computational Biology, Mines Paris-PSL, PSL Research University, 75006, Paris, France.,Institut Curie, 75248, Paris, France.,INSERM U900, 75428, Paris, France
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35
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The Solubility Studies and the Complexation Mechanism Investigations of Biologically Active Spiro[cyclopropane-1,3'-oxindoles] with β-Cyclodextrins. Pharmaceutics 2023; 15:pharmaceutics15010228. [PMID: 36678857 PMCID: PMC9861668 DOI: 10.3390/pharmaceutics15010228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
In this work, we first improved the aqueous solubility of biologically active spiro[cyclopropane-1,3′-oxindoles] (SCOs) via their complexation with different β-cyclodextrins (β-CDs) and proposed a possible mechanism of the complex formation. β-CDs significantly increased the water solubility of SCOs (up to fourfold). Moreover, the nature of the substituents in the β-CDs influenced the solubility of the guest molecule (MβCD > SBEβCD > HPβCD). Complexation preferably occurred via the inclusion of aromatic moieties of SCOs into the hydrophobic cavity of β-CDs by the numerous van der Waals contacts and formed stable supramolecular systems. The phase solubility technique and optical microscopy were used to determine the dissociation constants of the complexes (Kc~102 M−1) and reveal a significant decrease in the size of the formed crystals. FTIR-ATR microscopy, PXRD, and 1H-1H ROESY NMR measurements, as well as molecular modeling studies, were carried out to elucidate the host−guest interaction mechanism of the complexation. Additionally, in vitro experiments were carried out and revealed enhancements in the antibacterial activity of SCOs due to their complexation with β-CDs.
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36
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Liu X, Liu Y, Qiang L, Ren Y, Lin Y, Li H, Chen Q, Gao S, Yang X, Zhang C, Fan M, Zheng P, Li S, Wang J. Multifunctional 3D-printed bioceramic scaffolds: Recent strategies for osteosarcoma treatment. J Tissue Eng 2023; 14:20417314231170371. [PMID: 37205149 PMCID: PMC10186582 DOI: 10.1177/20417314231170371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/31/2023] [Indexed: 05/21/2023] Open
Abstract
Osteosarcoma is the most prevalent bone malignant tumor in children and teenagers. The bone defect, recurrence, and metastasis after surgery severely affect the life quality of patients. Clinically, bone grafts are implanted. Primary bioceramic scaffolds show a monomodal osteogenesis function. With the advances in three-dimensional printing technology and materials science, while maintaining the osteogenesis ability, scaffolds become more patient-specific and obtain additional anti-tumor ability with functional agents being loaded. Anti-tumor therapies include photothermal, magnetothermal, old and novel chemo-, gas, and photodynamic therapy. These strategies kill tumors through novel mechanisms to treat refractory osteosarcoma due to drug resistance, and some have shown the potential to reverse drug resistance and inhibit metastasis. Therefore, multifunctional three-dimensional printed bioceramic scaffolds hold excellent promise for osteosarcoma treatments. To better understand, we review the background of osteosarcoma, primary 3D-printed bioceramic scaffolds, and different therapies and have a prospect for the future.
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Affiliation(s)
- Xingran Liu
- Shanghai Key Laboratory of Orthopedic
Implant, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital,
Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
| | - Yihao Liu
- Shanghai Key Laboratory of Orthopedic
Implant, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital,
Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
| | - Lei Qiang
- Southwest Jiaotong University, Chengdu,
China
| | - Ya Ren
- Southwest Jiaotong University, Chengdu,
China
| | - Yixuan Lin
- Shanghai Key Laboratory of Orthopedic
Implant, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital,
Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Han Li
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
| | - Qiuhan Chen
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
| | - Shuxin Gao
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
| | - Xue Yang
- Southwest Jiaotong University, Chengdu,
China
| | - Changru Zhang
- Shanghai Key Laboratory of Orthopedic
Implant, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital,
Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
| | - Minjie Fan
- Department of Orthopaedic Surgery,
Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Pengfei Zheng
- Department of Orthopaedic Surgery,
Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Shuai Li
- Department of Orthopedics, The First
Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinwu Wang
- Shanghai Key Laboratory of Orthopedic
Implant, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital,
Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
- Southwest Jiaotong University, Chengdu,
China
- Shanghai Jiao Tong University,
Shanghai, China
- Weifang Medical University School of
Rehabilitation Medicine, Weifang, Shandong Province, China
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37
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Menezes Spadeto JP, Freitas MP, Cormanich RA. Fluorinated dihydropyridines as candidates to block L-type voltage-dependent calcium channels. J Biomol Struct Dyn 2022; 40:13456-13471. [PMID: 34720037 DOI: 10.1080/07391102.2021.1989039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Voltage-gated calcium (Cav) channels malfunction may lead to Alzheimer's and cardiovascular disorders, thus a critical protein target for drug development and treatment against several diseases. Indeed, dihydropyridines (DHPs) as nifedipine and amlodipine are top-selling pharmaceuticals and, respectively, the 121st and 5th most prescribed drugs in the United States that have been used as successful selective blockers for L-type Ca2+ channels (LCC) and may be helpful model structures to compare with new DHP analogs. In this context, we have performed a structure-based drug design (SBDD) study of several fluorinated DHPs by using homology modeling, molecular docking, quantitative structure activity relationship (QSAR) and molecular dynamics calculations. Such approaches combined with molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) interaction energy results and screening of ADMET (absorption, distribution, metabolism, excretion and toxicity) properties indicate that all ligands in this study are potential new candidates to be tested experimentally for inhibition of LCC and may have higher affinities than the commonly used drugs, being convenient synthetic routes proposed for 11-16, which are among the ligands that showed the best theoretical results concerning LCC inhibition. Furthermore, the ligand interactions with the binding site were carefully examined using the topological noncovalent interactions (NCI) method, which highlighted specifically responsible amino acid residues that increase the spontaneity of the new proposed DHP ligands.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- João Paulo Menezes Spadeto
- Department of Organic Chemistry, Laboratory of Experimental and Theoretical Organic Chemistry, Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
| | - Matheus P Freitas
- Department of Chemistry, Institute of Natural Sciences, Federal University of Lavras, Lavras, MG, Brazil
| | - Rodrigo A Cormanich
- Department of Organic Chemistry, Laboratory of Experimental and Theoretical Organic Chemistry, Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
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38
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Bogado ML, Villafañe RN, Gómez Chavez JL, Angelina EL, Sosa GL, Peruchena NM. Targeting Protein Pockets with Halogen Bonds: The Role of the Halogen Environment. J Chem Inf Model 2022; 62:6494-6507. [PMID: 36044012 DOI: 10.1021/acs.jcim.2c00475] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein pockets that form a halogen bond (X-bond) with a halogenated ligand molecule simultaneously form other (mainly hydrophobic) interactions with the halogen atom that can be considered as its "X-bond environment" (XBenv). Most studies in the field have focused on the X-bond, with the properties of the XBenv usually overlooked. In this work, we derived a protocol that evaluates the XBenv strength as a measure of the propensity of a protein pocket to host an X-bond. The charge density-based topological descriptors in combination with machine learning tools were employed to predict formation and strength of the interactions that conform the XBenv as a function of their geometrical parameters. On the basis of these results, we propose that the XBenv can be used as a footprint to judge the chance of a protein pocket to form an X-bond.
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Affiliation(s)
- María Lucrecia Bogado
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Roxana Noelia Villafañe
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - José Leonardo Gómez Chavez
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Emilio Luis Angelina
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Gladis Laura Sosa
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Nélida María Peruchena
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
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39
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Mizuguchi M, Nakagawa Y, Inui K, Katayama W, Sawai Y, Shimane A, Kitakami R, Okada T, Nabeshima Y, Yokoyama T, Kanamitsu K, Nakagawa S, Toyooka N. Chlorinated Naringenin Analogues as Potential Inhibitors of Transthyretin Amyloidogenesis. J Med Chem 2022; 65:16218-16233. [PMID: 36472374 DOI: 10.1021/acs.jmedchem.2c00511] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Misfolding and aggregation of transthyretin are implicated in the fatal systemic disease known as transthyretin amyloidosis. Here, we report the development of a naringenin derivative bearing two chlorine atoms that will be efficacious for preventing aggregation of transthyretin in the eye. The amyloid inhibitory activity of the naringenin derivative was as strong as that of tafamidis, which is the first therapeutic agent targeting transthyretin in the plasma. X-ray crystal structures of the compounds in complex with transthyretin demonstrated that the naringenin derivative with one chlorine bound to the thyroxine-binding site of transthyretin in the forward mode and that the derivative with two chlorines bound to it in the reverse mode. An ex vivo competitive binding assay showed that naringenin derivatives exhibited more potent binding than tafamidis in the plasma. Furthermore, an in vivo pharmacokinetic study demonstrated that the dichlorinated derivative was significantly delivered to the eye.
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Affiliation(s)
- Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Yusuke Nakagawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Japan
| | - Kishin Inui
- Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Wakana Katayama
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Yurika Sawai
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Ayaka Shimane
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Ryota Kitakami
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Takuya Okada
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Kayoko Kanamitsu
- Drug Discovery Initiative, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shinsaku Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Naoki Toyooka
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan
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40
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Winiewska-Szajewska M, Czapinska H, Kaus-Drobek M, Fricke A, Mieczkowska K, Dadlez M, Bochtler M, Poznański J. Competition between electrostatic interactions and halogen bonding in the protein-ligand system: structural and thermodynamic studies of 5,6-dibromobenzotriazole-hCK2α complexes. Sci Rep 2022; 12:18964. [PMID: 36347916 PMCID: PMC9641685 DOI: 10.1038/s41598-022-23611-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Abstract
CK2 is a member of the CMGC group of eukaryotic protein kinases and a cancer drug target. It can be efficiently inhibited by halogenated benzotriazoles and benzimidazoles. Depending on the scaffold, substitution pattern, and pH, these compounds are either neutral or anionic. Their binding poses are dictated by a hydrophobic effect (desolvation) and a tug of war between a salt bridge/hydrogen bond (to K68) and halogen bonding (to E114 and V116 backbone oxygens). Here, we test the idea that binding poses might be controllable by pH for ligands with near-neutral pKa, using the conditionally anionic 5,6-DBBt and constitutively anionic TBBt as our models. We characterize the binding by low-volume Differential Scanning Fluorimetry (nanoDSF), Isothermal Calorimetry (ITC), Hydrogen/Deuterium eXchange (HDX), and X-ray crystallography (MX). The data indicate that the ligand pose away from the hinge dominates for the entire tested pH range (5.5-8.5). The insensitivity of the binding mode to pH is attributed to the perturbation of ligand pKa upon binding that keeps it anionic in the ligand binding pocket at all tested pH values. However, a minor population of the ligand, detectable only by HDX, shifts towards the hinge in acidic conditions. Our findings demonstrate that electrostatic (ionic) interactions predominate over halogen bonding.
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Affiliation(s)
- Maria Winiewska-Szajewska
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.12847.380000 0004 1937 1290Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-089 Warsaw, Poland
| | - Honorata Czapinska
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.419362.bInternational Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Magdalena Kaus-Drobek
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Anna Fricke
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.419362.bInternational Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Kinga Mieczkowska
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Michał Dadlez
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Matthias Bochtler
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.419362.bInternational Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Jarosław Poznański
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
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41
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SAR study of oxidative DIMs analogs targeting the Nur77-mediated apoptotic pathway of cancer cells. Bioorg Chem 2022; 129:106156. [PMID: 36179441 DOI: 10.1016/j.bioorg.2022.106156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/21/2022] [Accepted: 09/12/2022] [Indexed: 11/21/2022]
Abstract
Nur77, an orphan nuclear receptor, is implicated in regulating diverse cellular biological processes including apoptosis and inflammation. We previously identified BI1071 (DIM-C-pPhCF3+MeSO3-), an oxidized methanesulfonate salt of (4-CF3-Ph-C-DIM), was a direct ligand of Nur77, which could activate the Nur77-Bcl-2 apoptotic pathway. To obtain more effective compounds targeting the Nur77-mediated apoptotic pathway, we designed and synthesized a series of BI1071 analogs by introducing various substituent groups in the indolyl-rings of BI1071. Structure-activity relationship study identified A11, B5 and B15 as improved analogs with stronger binding affinity to Nur77 and enhanced apoptotic activity compared to BI1071. Nur77-binding studies demonstrated that A11, B5 and B15 bind to Nur77 with a Kd of 34 nM, 19 nM and 16 nM, respectively. Furthermore, mechanism studies showed that A11, B5 and B15 induced apoptosis through utilizing the Nur77-Bcl-2 pathway.
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42
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Khiar-Fernández N, Zian D, Vázquez-Villa H, Martínez RF, Escobar-Peña A, Foronda-Sainz R, Ray M, Puigdomenech-Poch M, Cincilla G, Sánchez-Martínez M, Kihara Y, Chun J, López-Vales R, López-Rodríguez ML, Ortega-Gutiérrez S. Novel Antagonist of the Type 2 Lysophosphatidic Acid Receptor (LPA 2), UCM-14216, Ameliorates Spinal Cord Injury in Mice. J Med Chem 2022; 65:10956-10974. [PMID: 35948083 PMCID: PMC9421655 DOI: 10.1021/acs.jmedchem.2c00046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Spinal cord injuries (SCIs) irreversibly disrupt spinal
connectivity,
leading to permanent neurological disabilities. Current medical treatments
for reducing the secondary damage that follows the initial injury
are limited to surgical decompression and anti-inflammatory drugs,
so there is a pressing need for new therapeutic strategies. Inhibition
of the type 2 lysophosphatidic acid receptor (LPA2) has
recently emerged as a new potential pharmacological approach to decrease
SCI-associated damage. Toward validating this receptor as a target
in SCI, we have developed a new series of LPA2 antagonists,
among which compound 54 (UCM-14216) stands out as a potent
and selective LPA2 receptor antagonist (Emax = 90%, IC50 = 1.9 μM, KD = 1.3 nM; inactive at LPA1,3–6 receptors).
This compound shows efficacy in an in vivo mouse model of SCI in an
LPA2-dependent manner, confirming the potential of LPA2 inhibition for providing a new alternative for treating SCI.
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Affiliation(s)
- Nora Khiar-Fernández
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Debora Zian
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - R Fernando Martínez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Andrea Escobar-Peña
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Román Foronda-Sainz
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Manisha Ray
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maria Puigdomenech-Poch
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Institut de Neurociències, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de Barcelona, Bellaterra, BarcelonaE-08193, Spain
| | - Giovanni Cincilla
- Molomics, Barcelona Science Park, Baldiri i Reixac 4-8, Barcelona E-08028, Spain
| | - Melchor Sánchez-Martínez
- Molomics, Barcelona Science Park, Baldiri i Reixac 4-8, Barcelona E-08028, Spain.,Burua Scientific, Sant Pere de Ribes E-08810, Spain
| | - Yasuyuki Kihara
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jerold Chun
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Rubèn López-Vales
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Institut de Neurociències, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de Barcelona, Bellaterra, BarcelonaE-08193, Spain
| | - María L López-Rodríguez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Silvia Ortega-Gutiérrez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
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43
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Conformation and structural features of diuron and irgarol: insights from quantum chemistry calculations. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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44
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Ring replacement recommender: Ring modifications for improving biological activity. Eur J Med Chem 2022; 238:114483. [DOI: 10.1016/j.ejmech.2022.114483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/19/2022]
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45
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Pimviriyakul P, Pholert P, Somjitt S, Choowongkomon K. Role of conserved arginine in
HadA
monooxygenase for
4‐nitrophenol
and
4‐chlorophenol
detoxification. Proteins 2022; 90:1291-1302. [DOI: 10.1002/prot.26312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/18/2022]
Affiliation(s)
- Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science Kasetsart University Chatuchak Bangkok Thailand
| | - Patipan Pholert
- Department of Biochemistry, Faculty of Science Kasetsart University Chatuchak Bangkok Thailand
| | - Supamas Somjitt
- Department of Biochemistry, Faculty of Science Kasetsart University Chatuchak Bangkok Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science Kasetsart University Chatuchak Bangkok Thailand
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46
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Jena S, Dutta J, Tulsiyan KD, Sahu AK, Choudhury SS, Biswal HS. Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking. Chem Soc Rev 2022; 51:4261-4286. [PMID: 35560317 DOI: 10.1039/d2cs00133k] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Shubhranshu Shekhar Choudhury
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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Biodegradation of 3-Chloronitrobenzene and 3-Bromonitrobenzene by Diaphorobacter sp. Strain JS3051. Appl Environ Microbiol 2022; 88:e0243721. [PMID: 35343758 DOI: 10.1128/aem.02437-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Halonitrobenzenes are toxic chemical intermediates used widely for industrial synthesis of dyes and pesticides. Bacteria able to degrade 2- and 4-chloronitrobenzene have been isolated and characterized; in contrast, no natural isolate has been reported to degrade meta-halonitrobenzenes. In this study, Diaphorobacter sp. strain JS3051, previously reported to degrade 2,3-dichloronitrobenzene, grew readily on 3-chloronitrobenzene and 3-bromonitrobenzene, but not on 3-fluoronitrobenzene, as sole sources of carbon, nitrogen, and energy. A Rieske nonheme iron dioxygenase (DcbAaAbAcAd) catalyzed the dihydroxylation of 3-chloronitrobenzene and 3-bromonitrobenzene, resulting in the regiospecific production of ring-cleavage intermediates 4-chlorocatechol and 4-bromocatechol. The lower activity and relaxed regiospecificity of DcbAaAbAcAd toward 3-fluoronitrobenzene is likely due to the higher electronegativity of the fluorine atom, which hinders it from interacting with E204 residue at the active site. DccA, a chlorocatechol 1,2-dioxygenase, converts 4-chlorocatechol and 4-bromocatechol into the corresponding halomuconic acids with high catalytic efficiency, but with much lower Kcat/Km values for fluorocatechol analogues. The results indicate that the Dcb and Dcc enzymes of Diaphorobacter sp. strain JS3051 can catalyze the degradation of 3-chloro- and 3-bromonitrobenzene in addition to 2,3-dichloronitrobenzene. The ability to utilize multiple substrates would provide a strong selective advantage in a habitat contaminated with mixtures of chloronitrobenzenes. IMPORTANCE Halonitroaromatic compounds are persistent environmental contaminants, and some of them have been demonstrated to be degraded by bacteria. Natural isolates that degrade 3-chloronitrobenzene and 3-bromonitrobenzene have not been reported. In this study, we report that Diaphorobacter sp. strain JS3051 can degrade 2,3-dichloronitrobenzene, 3-chloronitrobenzene, and 3-bromonitrobenzene using the same catabolic pathway, whereas it is unable to grow on 3-fluoronitrobenzene. Based on biochemical analyses, it can be concluded that the initial dioxygenase and lower pathway enzymes are inefficient for 3-fluoronitrobenzene and even misroute the intermediates, which is likely responsible for the failure to grow. These results advance our understanding of how the broad substrate specificities of catabolic enzymes allow bacteria to adapt to habitats with mixtures of xenobiotic contaminants.
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Matulja D, Vranješević F, Kolympadi Markovic M, Pavelić SK, Marković D. Anticancer Activities of Marine-Derived Phenolic Compounds and Their Derivatives. Molecules 2022; 27:molecules27041449. [PMID: 35209235 PMCID: PMC8879422 DOI: 10.3390/molecules27041449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/15/2022] [Accepted: 02/19/2022] [Indexed: 12/24/2022] Open
Abstract
Since the middle of the last century, marine organisms have been identified as producers of chemically and biologically diverse secondary metabolites which have exerted various biological activities including anticancer, anti-inflammatory, antioxidant, antimicrobial, antifouling and others. This review primarily focuses on the marine phenolic compounds and their derivatives with potent anticancer activity, isolated and/or modified in the last decade. Reports on the elucidation of their structures as well as biosynthetic studies and total synthesis are also covered. Presented phenolic compounds inhibited cancer cells proliferation or migration, at sub-micromolar or nanomolar concentrations (lamellarins D (37), M (38), K (39), aspergiolide B (41), fradimycin B (62), makulavamine J (66), mayamycin (69), N-acetyl-N-demethylmayamycin (70) or norhierridin B (75)). In addition, they exhibited anticancer properties by a diverse biological mechanism including induction of apoptosis or inhibition of cell migration and invasive potential. Finally, phlorotannins 1–7 and bromophenols 12–29 represent the most researched phenolic compounds, of which the former are recognized as protective agents against UVB or gamma radiation-induced skin damages. Finally, phenolic metabolites were assorted into six main classes: phlorotannins, bromophenols, flavonoids, coumarins, terpenophenolics, quinones and hydroquinones. The derivatives that could not be attributed to any of the above-mentioned classes were grouped in a separate class named miscellaneous compounds.
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Affiliation(s)
- Dario Matulja
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, 51000 Rijeka, Croatia; (D.M.); (F.V.); (M.K.M.)
| | - Filip Vranješević
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, 51000 Rijeka, Croatia; (D.M.); (F.V.); (M.K.M.)
| | - Maria Kolympadi Markovic
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, 51000 Rijeka, Croatia; (D.M.); (F.V.); (M.K.M.)
| | - Sandra Kraljević Pavelić
- Faculty of Health Studies, University of Rijeka, Viktora Cara Emina 5, 51000 Rijeka, Croatia
- Correspondence: (S.K.P.); (D.M.); Tel.: +385-51-688-266 (S.K.P.); +385-91-500-8676 (D.M.)
| | - Dean Marković
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, 51000 Rijeka, Croatia; (D.M.); (F.V.); (M.K.M.)
- Correspondence: (S.K.P.); (D.M.); Tel.: +385-51-688-266 (S.K.P.); +385-91-500-8676 (D.M.)
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Dundar BA, Zora M. A facile synthesis of a novel family of heterotricyclic hybrids: Spiro-pyrrolopyridazines. SYNTHETIC COMMUN 2022. [DOI: 10.1080/00397911.2021.2024575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Buse Aysen Dundar
- Department of Chemistry, Middle East Technical University, Ankara, Turkey
| | - Metin Zora
- Department of Chemistry, Middle East Technical University, Ankara, Turkey
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Tan SL, Lo KM, Tan YS, Tiekink ERT. Structural systematics in the isomorphous binary co-crystal solvates comprising 2,2'-dithiodibenzoic acid, 4-halobenzoic acid and dimethylformamide (1:1:1), for halide = chloride, bromide and iodide. CrystEngComm 2022. [DOI: 10.1039/d2ce00094f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 1:1:1 binary co-crystal solvates formulated as 2,2'-dithiodibenzoic acid (DTBA), 4-halobenzoic acid (4-XBA) and dimethylformamide (DMF) for X = Cl (1), Br (2) and I (3) are isomorphous and the...
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