1
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Pees A, Tong J, Birudaraju S, Munot YS, Liang SH, Saturnino Guarino D, Mach RH, Mathis CA, Vasdev N. Development of Pyridothiophene Compounds for PET Imaging of α-Synuclein. Chemistry 2024; 30:e202303921. [PMID: 38354298 DOI: 10.1002/chem.202303921] [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: 11/27/2023] [Revised: 01/29/2024] [Accepted: 02/14/2024] [Indexed: 02/16/2024]
Abstract
Aggregated α-synuclein (α-syn) protein is a pathological hallmark of Parkinson's disease (PD) and Lewy body dementia (LBD). Development of positron emission tomography (PET) radiotracers to image α-syn aggregates has been a longstanding goal. This work explores the suitability of a pyridothiophene scaffold for α-syn PET radiotracers, where 47 derivatives of a potent pyridothiophene (asyn-44; Kd=1.85 nM) were synthesized and screened against [3H]asyn-44 in competitive binding assays using post-mortem PD brain homogenates. Equilibrium inhibition constant (Ki) values of the most potent compounds were determined, of which three had Ki's in the lower nanomolar range (12-15 nM). An autoradiography study confirmed that [3H]asyn-44 is promising for imaging brain sections from multiple system atrophy and PD donors. Fluorine-18 labelled asyn-44 was synthesized in 6±2 % radiochemical yield (decay-corrected, n=5) with a molar activity of 263±121 GBq/μmol. Preliminary PET imaging of [18F]asyn-44 in rats showed high initial brain uptake (>1.5 standardized uptake value (SUV)), moderate washout (~0.4 SUV at 60 min), and low variability. Radiometabolite analysis showed 60-80 % parent tracer in the brain after 30 and 60 mins. While [18F]asyn-44 displayed good in vitro properties and acceptable brain uptake, troublesome radiometabolites precluded further PET imaging studies. The synthesis and in vitro evaluation of additional pyridothiophene derivatives are underway, with the goal of attaining improved affinity and metabolic stability.
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Affiliation(s)
- Anna Pees
- Azrieli Centre for Neuro-Radiochemistry, Brain Health Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, ON M5T 1R8, Canada
| | - Junchao Tong
- Azrieli Centre for Neuro-Radiochemistry, Brain Health Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, ON M5T 1R8, Canada
| | | | | | - Steven H Liang
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, Georgia 30322, United States
| | - Dinahlee Saturnino Guarino
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, 1012, 231 S. 34th Street, Philadelphia, Pennsylvania, 19104-6323, United States
| | - Robert H Mach
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, 1012, 231 S. 34th Street, Philadelphia, Pennsylvania, 19104-6323, United States
| | - Chester A Mathis
- Department of Radiology, University of Pittsburgh, Pittsburgh, Pennsylvania, 15213, United States
| | - Neil Vasdev
- Azrieli Centre for Neuro-Radiochemistry, Brain Health Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, ON M5T 1R8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T-1R8, Canada
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2
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Das N, Roy J, Patra B, Saunders E, Sarkar D, Goon S, Sinha BP, Roy S, Roy S, Sarif J, Bandopadhyay P, Barik S, Mukherjee S, McNamara N, Varghese S, Simpson K, Baell J, McConville M, Ganguly D, Talukdar A. Hit-to-lead optimization of 2-aminoquinazolines as anti-microbial agents against Leishmania donovani. Eur J Med Chem 2024; 269:116256. [PMID: 38461679 DOI: 10.1016/j.ejmech.2024.116256] [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: 11/09/2023] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 03/12/2024]
Abstract
Visceral leishmaniasis is a potentially fatal disease caused by infection by the intracellular protist pathogens Leishmania donovani or Leishmania infantum. Present therapies are ineffective because of high costs, variable efficacy against different species, the requirement for hospitalization, toxicity and drug resistance. Detailed analysis of previously published hit molecules suggested a crucial role of 'guanidine' linkage for their efficacy against L. donovani. Here we report the design of 2-aminoquinazoline heterocycle as a basic pharmacophore-bearing guanidine linkage. The introduction of various groups and functionality at different positions of the quinazoline scaffold results in enhanced antiparasitic potency with modest host cell cytotoxicity using a physiologically relevant THP-1 transformed macrophage infection model. In terms of the ADME profile, the C7 position of quinazoline was identified as a guiding tool for designing better molecules. The good ADME profile of the compounds suggests that they merit further consideration as lead compounds for treating visceral leishmaniasis.
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Affiliation(s)
- Nirmal Das
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Jayasree Roy
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Binita Patra
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Eleanor Saunders
- Department of Biochemistry and Pharmacology, Bio21 Institute of Molecular Science and Biotechnology (Bio21), University of Melbourne, Parkville, Victoria 3052, Australia
| | - Dipika Sarkar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Sunny Goon
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Bishnu Prasad Sinha
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Shreya Roy
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Swarnali Roy
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Jafar Sarif
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Purbita Bandopadhyay
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Subhasis Barik
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Suravi Mukherjee
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Nicole McNamara
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 2052, Australia
| | - Swapna Varghese
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 2052, Australia
| | - Kaylene Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria 3000, Australia
| | - Jonathan Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 2052, Australia
| | - Malcolm McConville
- Department of Biochemistry and Pharmacology, Bio21 Institute of Molecular Science and Biotechnology (Bio21), University of Melbourne, Parkville, Victoria 3052, Australia
| | - Dipyaman Ganguly
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India.
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India.
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3
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Havrylyuk D, Heidary DK, Glazer EC. The Impact of Inorganic Systems and Photoactive Metal Compounds on Cytochrome P450 Enzymes and Metabolism: From Induction to Inhibition. Biomolecules 2024; 14:441. [PMID: 38672458 PMCID: PMC11048704 DOI: 10.3390/biom14040441] [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: 01/23/2024] [Revised: 03/25/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024] Open
Abstract
While cytochrome P450 (CYP; P450) enzymes are commonly associated with the metabolism of organic xenobiotics and drugs or the biosynthesis of organic signaling molecules, they are also impacted by a variety of inorganic species. Metallic nanoparticles, clusters, ions, and complexes can alter CYP expression, modify enzyme interactions with reductase partners, and serve as direct inhibitors. This commonly overlooked topic is reviewed here, with an emphasis on understanding the structural and physiochemical basis for these interactions. Intriguingly, while both organometallic and coordination compounds can act as potent CYP inhibitors, there is little evidence for the metabolism of inorganic compounds by CYPs, suggesting a potential alternative approach to evading issues associated with rapid modification and elimination of medically useful compounds.
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Affiliation(s)
| | - David K. Heidary
- Department of Chemistry, North Carolina State University, Raleigh, NC 27067, USA;
| | - Edith C. Glazer
- Department of Chemistry, North Carolina State University, Raleigh, NC 27067, USA;
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4
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Liu T, Padyana AK, Judd ET, Jin L, Hammoudeh D, Kung C, Dang L. Structure-Based Design of AG-946, a Pyruvate Kinase Activator. ChemMedChem 2024; 19:e202300559. [PMID: 38109501 DOI: 10.1002/cmdc.202300559] [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: 10/17/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
Pyruvate kinase (PK) is the enzyme that catalyzes the conversion of phosphoenolpyruvate and adenosine diphosphate to pyruvate and adenosine triphosphate in glycolysis and plays a crucial role in regulating cell metabolism. We describe the structure-based design of AG-946, an activator of PK isoforms, including red blood cell-specific forms of PK (PKR). This was designed to have a pseudo-C2-symmetry matching its allosteric binding site on the PK enzyme, which increased its potency toward PKR while reducing activity against off-targets observed from the original scaffold. AG-946 (1) demonstrated activation of human wild-type PK (half-maximal activation concentration [AC50 ]=0.005 μM) and a panel of mutated PK proteins (K410E [AC50 =0.0043 μM] and R510Q [AC50 =0.0069 μM]), (2) displayed a significantly longer half-time of activation (>150-fold) compared with 6-(3-methoxybenzyl)-4-methyl-2-(methylsulfinyl)-4,6-dihydro-5H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin-5-one, and (3) stabilized PKR R510Q, an unstable mutant PKR enzyme, and preserved its catalytic activity under increasingly denaturing conditions. As a potent, oral, small-molecule allosteric activator of wild-type and mutant PKR, AG-946 was advanced to human clinical trials.
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Affiliation(s)
- Tao Liu
- Ensem Therapeutics, 880 Winter St, Waltham, MA 02451, USA
| | | | - Evan T Judd
- Novartis Institute for Biomedical Research, 250 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Lei Jin
- Agios Pharmaceuticals, Inc., 88 Sidney St, Cambridge, MA, USA
| | - Dalia Hammoudeh
- Agios Pharmaceuticals Inc., 88 Sidney St, Cambridge, MA, USA
| | - Charles Kung
- Remix Therapeutics, 100 Forge Rd, Watertown, MA 02472, USA
| | - Lenny Dang
- Verolix, Inc., 800 Boylston St. Unit 900147, Boston, MA, 02199, USA
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5
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Yi X, Tran E, Odiba JO, Qin CX, Ritchie RH, Baell JB. The formyl peptide receptors FPR1 and FPR2 as targets for inflammatory disorders: recent advances in the development of small-molecule agonists. Eur J Med Chem 2024; 265:115989. [PMID: 38199163 DOI: 10.1016/j.ejmech.2023.115989] [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: 08/27/2023] [Revised: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Formyl peptide receptors (FPRs) comprise a class of chemoattractant pattern recognition receptors, for which several physiological functions like host-defences, as well as the regulation of inflammatory responses, have been ascribed. With accumulating evidence that agonism of FPR1/FPR2 can confer pro-resolution of inflammation, increased attention from academia and industry has led to the discovery of new and interesting small-molecule FPR1/FPR2 agonists. Focused attention on the development of appropriate physicochemical and pharmacokinetic profiles is yielding synthesis of new compounds with promising in vivo readouts. This review presents an overview of small-molecule FPR1/FPR2 agonist medicinal chemistry developed over the past 20 years, with a particular emphasis on interrogation in the increasingly sophisticated bioassays which have been developed.
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Affiliation(s)
- Xiangyan Yi
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Eric Tran
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Jephthah O Odiba
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Cheng Xue Qin
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Victoria, 3052, Australia; Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, Victoria, 3004, Australia.
| | - Rebecca H Ritchie
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Victoria, 3052, Australia; Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, Victoria, 3004, Australia.
| | - Jonathan B Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia.
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6
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Cui Q, Huang C, Liu JY, Zhang JT. Small Molecule Inhibitors Targeting the "Undruggable" Survivin: The Past, Present, and Future from a Medicinal Chemist's Perspective. J Med Chem 2023; 66:16515-16545. [PMID: 38092421 DOI: 10.1021/acs.jmedchem.3c01130] [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] [Indexed: 12/29/2023]
Abstract
Survivin, a homodimeric protein and a member of the IAP family, plays a vital function in cell survival and cycle progression by interacting with various proteins and complexes. Its expression is upregulated in cancers but not detectable in normal tissues. Thus, it has been regarded and validated as an ideal cancer target. However, survivin is "undruggable" due to its lack of enzymatic activities or active sites for small molecules to bind/inhibit. Academic and industrial laboratories have explored different strategies to overcome this hurdle over the past two decades, with some compounds advanced into clinical testing. These strategies include inhibiting survivin expression, its interaction with binding partners and homodimerization. Here, we provide comprehensive analyses of these strategies and perspective on different small molecule survivin inhibitors to help drug discovery targeting "undruggable" proteins in general and survivin specifically with a true survivin inhibitor that will prevail in the foreseeable future.
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Affiliation(s)
- Qingbin Cui
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio 43614, United States
| | - Caoqinglong Huang
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio 43614, United States
| | - Jing-Yuan Liu
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio 43614, United States
| | - Jian-Ting Zhang
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio 43614, United States
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7
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Li B, Ruffoni A, Leonori D. A Photochemical Strategy for ortho-Aminophenol Synthesis via Dearomative-Rearomative Coupling Between Aryl Azides and Alcohols. Angew Chem Int Ed Engl 2023; 62:e202310540. [PMID: 37926921 DOI: 10.1002/anie.202310540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Abstract
ortho-Aminophenols are aromatic derivatives featuring vicinal N- and O-based functionalities commonly found in the structures of many high-value materials. These molecules are generally prepared using multistep strategies that follow the rules of electrophilic aromatic substitution (SE Ar) chemistry. Despite their high fidelity, such approaches cannot target substrates featuring a "contra-SE Ar" arrangement of N- and O-groups. Here we report an alternative strategy for the preparation of such ortho-aminophenols using aryl azides as the precursors. The process utilizes low-energy photoexcitation to trigger the decomposition of aryl azides into singlet nitrenes that undergo a dearomative-rearomative sequence. This allows the incorporation of alcoholic nucleophiles into a seven-membered ring azepine intermediate via temporary disruption of aromaticity, followed by electrophile-induced re-aromatization. The net retrosynthetic logic is that the alcohol displaces the azide, which, in turn, moves to its ortho position and furthermore is converted into an amide. The synthetic value and complementarity of this strategy has been demonstrated by the coupling of aryl azides with complex, drug-like alcohols and phenols as well as amines, thiols and thiophenols, which provides a general platform for the fast and selective heterofunctionalization of aromatics.
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Affiliation(s)
- Bo Li
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056, Aachen, Germany
| | - Alessandro Ruffoni
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056, Aachen, Germany
| | - Daniele Leonori
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056, Aachen, Germany
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8
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Wu T, Chen Y, Yang C, Lu M, Geng F, Guo J, Pi Y, Ling Y, Xu J, Cai T, Lu L, Zhou Y. Systematical Evaluation of the Structure-Cardiotoxicity Relationship of 7-Azaindazole-based PI3K Inhibitors Designed by Bioisosteric Approach. Cardiovasc Toxicol 2023; 23:364-376. [PMID: 37787964 DOI: 10.1007/s12012-023-09809-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023]
Abstract
A growing concern of cardiotoxicity induced by PI3K inhibitors has raised the requirements to evaluate the structure-cardiotoxicity relationship (SCR) in the development process of novel inhibitors. Based on three bioisosteric 7-azaindazole-based candidate inhibitors namely FD269, FD268 and FD274 that give same order of inhibitory concentration 50% (IC50) magnitude against PI3Ks, in this work, we proposed to systematically evaluate the SCR of 7-azaindazole-based PI3K inhibitors designed by bioisosteric approach. The 24-h lethal concentrations 50% (LC50) of FD269, FD268 and FD274 against zebrafish embryos were 0.35, 4.82 and above 50 μM (not detected), respectively. Determination of the heart rate, pericardial and yolk-sac areas and vascular malformation confirmed the remarkable reduction in the cardiotoxicity of from FD269 to FD268 and to FD274. The IC50s of all three compounds against the hERG channel were tested on the CHO cell line that constitutively expressing hERG channel, which were all higher than 20 μM. The transcriptomic analysis revealed that FD269 and FD268 induced the up-regulation of noxo1b, which encodes a subunit of an NADPH oxidase evoking the oxidative stress. Furthermore, immunohistochemistry tests confirmed the structure-dependent attenuation of the overproduction of ROS and cardiac apoptosis. Our results verified the feasibility of bioisosteric replacement to attenuate the cardiotoxicity of 7-azaindazole-based PI3K inhibitors, suggesting that the screening for PI3K inhibitors with both high potency and low cardiotoxicity from bioisosteres would be a beneficial trial.
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Affiliation(s)
- Tianze Wu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Yi Chen
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Chengbin Yang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Mingzhu Lu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Fang Geng
- School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jianhua Guo
- School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yan Pi
- School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yun Ling
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Jun Xu
- ABA Chemicals Co., Ltd, Taicang, 215400, Jiangsu, China
| | - Tong Cai
- ABA Chemicals Co., Ltd, Taicang, 215400, Jiangsu, China
| | - Lei Lu
- School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yaming Zhou
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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9
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Bennett JM, Ward KE, Muir RK, Kabeche S, Yoo E, Yeo T, Lam G, Zhang H, Almaliti J, Berger G, Faucher FF, Lin G, Gerwick WH, Yeh E, Fidock DA, Bogyo M. Covalent Macrocyclic Proteasome Inhibitors Mitigate Resistance in Plasmodium falciparum. ACS Infect Dis 2023; 9:2036-2047. [PMID: 37712594 PMCID: PMC10591878 DOI: 10.1021/acsinfecdis.3c00310] [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] [Indexed: 09/16/2023]
Abstract
The Plasmodium proteasome is a promising antimalarial drug target due to its essential role in all parasite lifecycle stages. Furthermore, proteasome inhibitors have synergistic effects when combined with current first-line artemisinin and related analogues. Linear peptides that covalently inhibit the proteasome are effective at killing parasites and have a low propensity for inducing resistance. However, these scaffolds generally suffer from poor pharmacokinetics and bioavailability. Here we describe the development of covalent, irreversible, macrocyclic inhibitors of the Plasmodium falciparum proteasome. We identified compounds with excellent potency and low cytotoxicity; however, the first generation suffered from poor microsomal stability. Further optimization of an existing macrocyclic scaffold resulted in an irreversible covalent inhibitor carrying a vinyl sulfone electrophile that retained high potency and low cytotoxicity and had acceptable metabolic stability. Importantly, unlike the parent reversible inhibitor that selected for multiple mutations in the proteasome, with one resulting in a 5,000-fold loss of potency, the irreversible analogue only showed a 5-fold loss in potency for any single point mutation. Furthermore, an epoxyketone analogue of the same scaffold retained potency against a panel of known proteasome mutants. These results confirm that macrocycles are optimal scaffolds to target the malarial proteasome and that the use of a covalent electrophile can greatly reduce the ability of the parasite to generate drug resistance mutations.
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Affiliation(s)
- John M Bennett
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Kurt E Ward
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York 10032, United States
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, New York 10032, United States
| | - Ryan K Muir
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Stephanie Kabeche
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Euna Yoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York 10032, United States
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, New York 10032, United States
| | - Grace Lam
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California 94304, United States
| | - Hao Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Jehad Almaliti
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Gabriel Berger
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Franco F Faucher
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Gang Lin
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92037, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Ellen Yeh
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94304, United States
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York 10032, United States
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, New York 10032, United States
- Division of Infectious Diseases, Columbia University Medical Center, New York, New York 10032, United States
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92037, United States
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10
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Evarts MM, Strong ZH, Krische MJ. Oxetane-, Azetidine-, and Bicyclopentane-Bearing N-Heterocycles from Ynones: Scaffold Diversification via Ruthenium-Catalyzed Oxidative Alkynylation. Org Lett 2023; 25:5907-5910. [PMID: 37527501 PMCID: PMC10445484 DOI: 10.1021/acs.orglett.3c02213] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
A process for 3-fold scaffold diversification is achieved via ruthenium-catalyzed oxidative alkynylation of commercially available oxetanols, azetidinols and bicyclopentanols to form α,β-acetylenic ketones (ynones), which are subsequently converted to oxetane-, azetidine- and bicyclopentane-bearing pyrazoles, isoxazoles and pyrimidines. A one-pot oxidative alkynylation-condensation protocol that directly converts azetidinols to azetidine-substituted pyrazoles or pyrimidines is demonstrated.
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Affiliation(s)
- Madeline M Evarts
- University of Texas at Austin, Department of Chemistry, Austin, Texas 78712, United States
| | - Zachary H Strong
- University of Texas at Austin, Department of Chemistry, Austin, Texas 78712, United States
| | - Michael J Krische
- University of Texas at Austin, Department of Chemistry, Austin, Texas 78712, United States
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11
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Trifonov AV, Gazizov AS, Tapalova AS, Kibardina LK, Appazov NO, Voloshina AD, Sapunova AS, Luybina AP, Abyzbekova GM, Dobrynin AB, Litvinov IA, Tauekel AK, Yespenbetova SO, Burilov AR, Pudovik MA. Synthesis and Anticancer Evaluation of Novel 7-Aza-Coumarine-3-Carboxamides. Int J Mol Sci 2023; 24:9927. [PMID: 37373075 DOI: 10.3390/ijms24129927] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Herein, we report the design and synthesis of novel 7-aza-coumarine-3-carboxamides via scaffold-hopping strategy and evaluation of their in vitro anticancer activity. Additionally, the improved non-catalytic synthesis of 7-azacoumarin-3-carboxylic acid is reported, which features water as the reaction medium and provides a convenient alternative to the known methods. The anticancer activity of the most potent 7-aza-coumarine-3-carboxamides against the HuTu 80 cell line is equal to that of reference Doxorubicin, while the selectivity towards the normal cell line is 9-14 fold higher.
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Affiliation(s)
- Alexey V Trifonov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russia
| | - Almir S Gazizov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russia
| | - Anipa S Tapalova
- Korkyt Ata Kyzylorda University, Aiteke Bi Street, 29A, Kyzylorda 120014, Kazakhstan
| | - Lyudmila K Kibardina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russia
| | - Nurbol O Appazov
- Korkyt Ata Kyzylorda University, Aiteke Bi Street, 29A, Kyzylorda 120014, Kazakhstan
| | - Alexandra D Voloshina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russia
| | - Anastasiia S Sapunova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russia
| | - Anna P Luybina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russia
| | - Gulmira M Abyzbekova
- Korkyt Ata Kyzylorda University, Aiteke Bi Street, 29A, Kyzylorda 120014, Kazakhstan
| | - Alexey B Dobrynin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russia
| | - Igor A Litvinov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russia
| | - Akerke K Tauekel
- Department of Oil, Chemistry and Nanotechnology, Kazan National Research Technological University, Karl Marx Str., 68, Kazan 420015, Russia
| | | | - Alexander R Burilov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russia
| | - Michail A Pudovik
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Science, Arbuzova Str., 8, Kazan 420088, Russia
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12
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Broni E, Striegel A, Ashley C, Sakyi PO, Peracha S, Velazquez M, Bebla K, Sodhi M, Kwofie SK, Ademokunwa A, Khan S, Miller WA. Molecular Docking and Dynamics Simulation Studies Predict Potential Anti-ADAR2 Inhibitors: Implications for the Treatment of Cancer, Neurological, Immunological and Infectious Diseases. Int J Mol Sci 2023; 24:ijms24076795. [PMID: 37047766 PMCID: PMC10095294 DOI: 10.3390/ijms24076795] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023] Open
Abstract
Altered RNA editing has been linked to several neurodevelopmental disorders, including autism spectrum disorder (ASD) and intellectual disability, in addition to depression, schizophrenia, some cancers, viral infections and autoimmune disorders. The human ADAR2 is a potential therapeutic target for managing these various disorders due to its crucial role in adenosine to inosine editing. This study applied consensus scoring to rank potential ADAR2 inhibitors after performing molecular docking with AutoDock Vina and Glide (Maestro), using a library of 35,161 compounds obtained from traditional Chinese medicine. A total of 47 compounds were predicted to be good binders of the human ADAR2 and had insignificant toxicity concerns. Molecular dynamics (MD) simulations, including the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) procedure, also emphasized the binding of the shortlisted compounds. The potential compounds had plausible binding free energies ranging from −81.304 to −1068.26 kJ/mol from the MM/PBSA calculations. ZINC000085511995, a naphthoquinone had more negative binding free energy (−1068.26 kJ/mol) than inositol hexakisphosphate (IHP) [−873.873 kJ/mol], an agonist and a strong binder of ADAR2. The potential displacement of IHP by ZINC000085511995 in the IHP binding site of ADAR2 could be explored for possible deactivation of ADAR2. Bayesian-based biological activity prediction corroborates the neuropharmacological, antineoplastic and antiviral activity of the potential lead compounds. All the potential lead compounds, except ZINC000014612330 and ZINC000013462928, were predicted to be inhibitors of various deaminases. The potential lead compounds also had probability of activity (Pa) > 0.442 and probability of inactivity (Pi) < 0.116 values for treating acute neurologic disorders, except for ZINC000085996580 and ZINC000013462928. Pursuing these compounds for their anti-ADAR2 activities holds a promising future, especially against neurological disorders, some cancers and viral infections caused by RNA viruses. Molecular interaction, hydrogen bond and per-residue decomposition analyses predicted Arg400, Arg401, Lys519, Trp687, Glu689, and Lys690 as hot-spot residues in the ADAR2 IHP binding site. Most of the top compounds were observed to have naphthoquinone, indole, furanocoumarin or benzofuran moieties. Serotonin and tryptophan, which are beneficial in digestive regulation, improving sleep cycle and mood, are indole derivatives. These chemical series may have the potential to treat neurological disorders, prion diseases, some cancers, specific viral infections, metabolic disorders and eating disorders through the disruption of ADAR2 pathways. A total of nine potential lead compounds were shortlisted as plausible modulators of ADAR2.
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Affiliation(s)
- Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Andrew Striegel
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Chemical and Biochemistry, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Carolyn Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Patrick O. Sakyi
- Department of Chemistry, School of Physical and Mathematical Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 56, Ghana
- Department of Chemical Sciences, School of Sciences, University of Energy and Natural Resources, Sunyani P.O. Box 214, Ghana
| | - Saqib Peracha
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Miriam Velazquez
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Kristeen Bebla
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Monsheel Sodhi
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Adesanya Ademokunwa
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Cognitive and Behavioral Neuroscience, Loyola University Chicago, Chicago, IL 60660, USA
| | - Sufia Khan
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
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Wiedemeyer SJA, Wu G, Pham TLP, Lang-Henkel H, Perez Urzua B, Whisstock JC, Law RHP, Steinmetzer T. Synthesis and Structural Characterization of Macrocyclic Plasmin Inhibitors. ChemMedChem 2023; 18:e202200632. [PMID: 36710259 DOI: 10.1002/cmdc.202200632] [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: 11/21/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023]
Abstract
Two series of macrocyclic plasmin inhibitors with a C-terminal benzylamine group were synthesized. The substitution of the N-terminal phenylsulfonyl group of a previously described inhibitor provided two analogues with sub-nanomolar inhibition constants. Both compounds possess a high selectivity against all other tested trypsin-like serine proteases. Furthermore, a new approach was used to selectively introduce asymmetric linker segments. Two of these compounds inhibit plasmin with Ki values close to 2 nM. For the first time, four crystal structures of these macrocyclic inhibitors could be determined in complex with a Ser195Ala microplasmin mutant. The macrocyclic core segment of the inhibitors binds to the open active site of plasmin without any steric hindrance. This binding mode is incompatible with other trypsin-like serine proteases containing a sterically demanding 99-hairpin loop. The crystal structures obtained experimentally explain the excellent selectivity of this inhibitor type as previously hypothesized.
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Affiliation(s)
- Simon J A Wiedemeyer
- Department of Pharmacy Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Guojie Wu
- Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology, Monash University, Melbourne, 3800, Australia
| | - T L Phuong Pham
- Department of Pharmacy Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Heike Lang-Henkel
- Department of Pharmacy Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Benjamin Perez Urzua
- Department of Cellular and Molecular Biology Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - James C Whisstock
- Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology, Monash University, Melbourne, 3800, Australia
| | - Ruby H P Law
- Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology, Monash University, Melbourne, 3800, Australia
| | - Torsten Steinmetzer
- Department of Pharmacy Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
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Dzedulionytė K, Fuxreiter N, Schreiber-Brynzak E, Žukauskaitė A, Šačkus A, Pichler V, Arbačiauskienė E. Pyrazole-based lamellarin O analogues: synthesis, biological evaluation and structure-activity relationships. RSC Adv 2023; 13:7897-7912. [PMID: 36909769 PMCID: PMC9999251 DOI: 10.1039/d3ra00972f] [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] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
A library of pyrazole-based lamellarin O analogues was synthesized from easily accessible 3(5)-aryl-1H-pyrazole-5(3)-carboxylates which were subsequently modified by bromination, N-alkylation and Pd-catalysed Suzuki cross-coupling reactions. Synthesized ethyl and methyl 3,4-diaryl-1-(2-aryl-2-oxoethyl)-1H-pyrazole-5-carboxylates were evaluated for their physicochemical property profiles and in vitro cytotoxicity against three human colorectal cancer cell lines HCT116, HT29, and SW480. The most active compounds inhibited cell proliferation in a low micromolar range. Selected ethyl 3,4-diaryl-1-(2-aryl-2-oxoethyl)-1H-pyrazole-5-carboxylates were further investigated for their mode of action. Results of combined viability staining via Calcein AM/Hoechst/PI and fluorescence-activated cell sorting data indicated that cell death was triggered in a non-necrotic manner mediated by mainly G2/M-phase arrest.
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Affiliation(s)
- Karolina Dzedulionytė
- Department of Organic Chemistry, Faculty of Chemical Technology, Kaunas University of Technology Radvilėnų pl. 19 LT-50254 Kaunas Lithuania
| | - Nina Fuxreiter
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna Althanstraße 14 1090 Vienna Austria
| | - Ekaterina Schreiber-Brynzak
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna Althanstraße 14 1090 Vienna Austria
| | - Asta Žukauskaitė
- Department of Chemical Biology, Faculty of Science, Palacký University Šlechtitelů 27 CZ-78371 Olomouc Czech Republic
| | - Algirdas Šačkus
- Department of Organic Chemistry, Faculty of Chemical Technology, Kaunas University of Technology Radvilėnų pl. 19 LT-50254 Kaunas Lithuania .,Institute of Synthetic Chemistry, Faculty of Chemical Technology, Kaunas University of Technology K. Baršausko g. 59 LT-51423 Kaunas Lithuania
| | - Verena Pichler
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna Althanstraße 14 1090 Vienna Austria
| | - Eglė Arbačiauskienė
- Department of Organic Chemistry, Faculty of Chemical Technology, Kaunas University of Technology Radvilėnų pl. 19 LT-50254 Kaunas Lithuania
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15
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Callis TB, Garrett TR, Montgomery AP, Danon JJ, Kassiou M. Recent Scaffold Hopping Applications in Central Nervous System Drug Discovery. J Med Chem 2022; 65:13483-13504. [PMID: 36206553 DOI: 10.1021/acs.jmedchem.2c00969] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The concept of bioisosterism and the implementation of bioisosteric replacement is fundamental to medicinal chemistry. The exploration of bioisosteres is often used to probe key structural features of candidate pharmacophores and enhance pharmacokinetic properties. As the understanding of bioisosterism has evolved, capabilities to undertake more ambitious bioisosteric replacements have emerged. Scaffold hopping is a broadly used term in the literature referring to a variety of different bioisosteric replacement strategies, ranging from simple heterocyclic replacements to topological structural overhauls. In this work, we have highlighted recent applications of scaffold hopping in the central nervous system drug discovery space. While we have highlighted the benefits of using scaffold hopping approaches in central nervous system drug discovery, these are also widely applicable to other medicinal chemistry fields. We also recommend a shift toward the use of more refined and meaningful terminology within the realm of scaffold hopping.
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Affiliation(s)
- Timothy B Callis
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Taylor R Garrett
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Jonathan J Danon
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Michael Kassiou
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
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16
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Chen M, Li Z, Shao X, Maienfisch P. Scaffold-Hopping Approach To Identify New Chemotypes of Dimpropyridaz. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11109-11122. [PMID: 35412307 DOI: 10.1021/acs.jafc.2c00636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Dimpropyridaz is a pyrazole carboxamide insecticide with a novel mode of action, currently under worldwide development by BASF, providing excellent activity against sucking pests. A series of dimpropyridaz analogues were designed to investigate the impact of bioisosteric heterocyclic replacements on the biological activity and molecular properties. Focus was given to prepare analogues where the 4-pyridazinyl moiety was replaced by 5-pyrimidinyl, 2-pyrimidinyl, 3-pyridazinyl, and 2-pyrazinyl groups. Five different synthetic routes were developed for the preparation of these analogues, delivering the target compounds in moderate to good yields. We explained some aspects of the observed structure-activity relationship by a density functional theory (DFT) calculation and DFT-derived Multiwfn and VMD program models. These findings provide first insights into the important role of the 4-pyridazinyl heterocyclic moiety in the pyrazole carboxamide insecticide chemical class and the mechanism of action of dimpropyridaz.
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Affiliation(s)
- Meijun Chen
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Xusheng Shao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Peter Maienfisch
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- CreInSol Consulting & Biocontrols, CH-4118 Rodersdorf, Switzerland
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Lee S, Jena R, Odom AL. Substituted pyridines from isoxazoles: scope and mechanism. Org Biomol Chem 2022; 20:6630-6636. [PMID: 35924784 DOI: 10.1039/d2ob00779g] [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
Treatment of isoxazoles with enamines leads to an inverse electron-demand hetero-Diels-Alder reaction that produces substituted pyridines in the presence of TiCl4(THF)2 and titanium powder. The reaction is highly regioselective with only a single isomer of the product observed by GC/MS and tolerant of many common functional groups. The transformation was examined computationally, and it was found that TiCl4 (or a similar Lewis acid) likely acts to catalyze the reaction. After the initial [4 + 2]-cycloaddition, the oxaza-[2.2.1]-bicycle produced likely ring opens before amine loss to give an N-oxide. The pyridine is then obtained after reduction with TiCl4 and titanium powder.
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Affiliation(s)
- Seokjoo Lee
- Michigan State University, Department of Chemistry, 578 S. Shaw Ln, East Lansing, Michigan 48824, USA.
| | - Rashmi Jena
- Michigan State University, Department of Chemistry, 578 S. Shaw Ln, East Lansing, Michigan 48824, USA.
| | - Aaron L Odom
- Michigan State University, Department of Chemistry, 578 S. Shaw Ln, East Lansing, Michigan 48824, USA.
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18
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Design, Synthesis and Biological Investigation of 2-Anilino Triazolopyrimidines as Tubulin Polymerization Inhibitors with Anticancer Activities. Pharmaceuticals (Basel) 2022; 15:ph15081031. [PMID: 36015179 PMCID: PMC9415608 DOI: 10.3390/ph15081031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
A further investigation aiming to generate new potential antitumor agents led us to synthesize a new series of twenty-two compounds characterized by the presence of the 7-(3',4',5'-trimethoxyphenyl)-[1,2,4]triazolo[1,5-a]pyrimidine pharmacophore modified at its 2-position. Among the synthesized compounds, three were significantly more active than the others. These bore the substituents p-toluidino (3d), p-ethylanilino (3h) and 3',4'-dimethylanilino (3f), and these compounds had IC50 values of 30-43, 160-240 and 67-160 nM, respectively, on HeLa, A549 and HT-29 cancer cells. The p-toluidino derivative 3d was the most potent inhibitor of tubulin polymerization (IC50: 0.45 µM) and strongly inhibited the binding of colchicine to tubulin (72% inhibition), with antiproliferative activity superior to CA-4 against A549 and HeLa cancer cell lines. In vitro investigation showed that compound 3d was able to block treated cells in the G2/M phase of the cell cycle and to induce apoptosis following the intrinsic pathway, further confirmed by mitochondrial depolarization and caspase-9 activation. In vivo experiments conducted on the zebrafish model showed good activity of 3d in reducing the mass of a HeLa cell xenograft. These effects occurred at nontoxic concentrations to the animal, indicating that 3d merits further developmental studies.
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Martínez-Peña F, Pearson AD, Tang EL, Kuburich NA, Mani SA, Schultz PG, Bollong MJ, Lairson LL. Synthesis and biological evaluation of novel FiVe1 derivatives as potent and selective agents for the treatment of mesenchymal cancers. Eur J Med Chem 2022; 242:114638. [PMID: 36001933 PMCID: PMC10377566 DOI: 10.1016/j.ejmech.2022.114638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/29/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
Epithelial-mesenchymal transition (EMT) endows stem cell-like properties to cancer cells. Targeting this process represents a potential therapeutic approach to overcome cancer metastasis and chemotherapy resistance. FiVe1 was identified from an EMT-based synthetic lethality screen and was found to inhibit the stem cell-like properties and proliferation of not only cancer cells undergoing EMT, but also more broadly in mesenchymal cancers that include therapeutically intractable soft tissue sarcomas. FiVe1 functions by directly binding to the type III intermediate filament protein vimentin (VIM) in a mode that induces hyperphosphorylation of Ser56, which results in selective disruption of mitosis and induced multinucleation in transformed VIM-expressing mesenchymal cancer cell types. Cell-based potency (IC50 = 1.6 μM, HT-1080 fibrosarcoma), poor solubility (<1 μM) and low oral bioavailability limits the direct application of FiVe1 as an in vivo probe or therapeutic agent. To overcome these drawbacks, we performed structure-activity relationship (SAR) studies and synthesized a set of 35 new compounds, consisting of diverse modifications of the FiVe1 scaffold. Among these compounds, 4e showed a marked improvement in potency (IC50 = 44 nM, 35-fold improvement, HT-1080) and cell type selectivity (19-fold improvement), when compared to FiVe1. Improvements in the potency of 4e, in terms of overall cytotoxicity, directly correlate with VIM Ser56 phosphorylation status and the oral bioavailability and pharmacokinetic profiles of 4e in mouse are superior to FiVe1. Successful optimization also resulted in potent and selective derivatives 11a, 11j and 11k, which exhibited superior pharmacological profiles, in terms of metabolic stability and aqueous solubility. Collectively, these optimization efforts have resulted in the development of promising FiVe1 analogs with potential applications in the treatment of mesenchymal cancers, as well as in the study of VIM-related biology.
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20
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Leino TO, Sieger P, Yli-Kauhaluoma J, Wallén EA, Kley JT. The azulene scaffold from a medicinal chemist's perspective: Physicochemical and in vitro parameters relevant for drug discovery. Eur J Med Chem 2022; 237:114374. [DOI: 10.1016/j.ejmech.2022.114374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/11/2022]
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21
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Hit-to-lead optimization of novel phenyl imidazole carboxamides that are active against Leishmania donovani. Eur J Med Chem 2022; 240:114577. [DOI: 10.1016/j.ejmech.2022.114577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 11/20/2022]
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22
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Zheng C, Holden D, Zheng MQ, Pracitto R, Wilcox KC, Lindemann M, Felchner Z, Zhang L, Tong J, Fowles K, Finnema SJ, Nabulsi N, Carson RE, Huang Y, Cai Z. A metabolically stable PET tracer for imaging synaptic vesicle protein 2A: synthesis and preclinical characterization of [ 18F]SDM-16. Eur J Nucl Med Mol Imaging 2022; 49:1482-1496. [PMID: 34761284 PMCID: PMC8940841 DOI: 10.1007/s00259-021-05597-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/17/2021] [Indexed: 11/01/2022]
Abstract
PURPOSE To quantify the synaptic vesicle glycoprotein 2A (SV2A) changes in the whole central nervous system (CNS) under pathophysiological conditions, a high affinity SV2A PET radiotracer with improved in vivo stability is desirable to minimize the potential confounding effect of radiometabolites. The aim of this study was to develop such a PET tracer based on the molecular scaffold of UCB-A, and evaluate its pharmacokinetics, in vivo stability, specific binding, and nonspecific binding signals in nonhuman primate brains, in comparison with [11C]UCB-A, [11C]UCB-J, and [18F]SynVesT-1. METHODS The racemic SDM-16 (4-(3,5-difluorophenyl)-1-((2-methyl-1H-imidazol-1-yl)methyl)pyrrolidin-2-one) and its two enantiomers were synthesized and assayed for in vitro binding affinities to human SV2A. We synthesized the enantiopure [18F]SDM-16 using the corresponding enantiopure arylstannane precursor. Nonhuman primate brain PET scans were performed on FOCUS 220 scanners. Arterial blood was drawn for the measurement of plasma free fraction (fP), radiometabolite analysis, and construction of the plasma input function. Regional time-activity curves (TACs) were fitted with the one-tissue compartment (1TC) model to obtain the volume of distribution (VT). Nondisplaceable binding potential (BPND) was calculated using either the nondisplaceable volume of distribution (VND) or the centrum semiovale (CS) as the reference region. RESULTS SDM-16 was synthesized in 3 steps with 44% overall yield and has the highest affinity (Ki = 0.9 nM) to human SV2A among all reported SV2A ligands. [18F]SDM-16 was prepared in about 20% decay-corrected radiochemical yield within 90 min, with greater than 99% radiochemical and enantiomeric purity. This radiotracer displayed high specific binding in monkey brains and was metabolically more stable than the other SV2A PET tracers. The fP of [18F]SDM-16 was 69%, which was higher than those of [11C]UCB-J (46%), [18F]SynVesT-1 (43%), [18F]SynVesT-2 (41%), and [18F]UCB-H (43%). The TACs were well described with the 1TC. The averaged test-retest variability (TRV) was 7 ± 3%, and averaged absolute TRV (aTRV) was 14 ± 7% for the analyzed brain regions. CONCLUSION We have successfully synthesized a novel SV2A PET tracer [18F]SDM-16, which has the highest SV2A binding affinity and metabolical stability among published SV2A PET tracers. The [18F]SDM-16 brain PET images showed superb contrast between gray matter and white matter. Moreover, [18F]SDM-16 showed high specific and reversible binding in the NHP brains, allowing for the reliable and sensitive quantification of SV2A, and has potential applications in the visualization and quantification of SV2A beyond the brain.
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Affiliation(s)
- Chao Zheng
- PET Center, Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Daniel Holden
- PET Center, Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Ming-Qiang Zheng
- PET Center, Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Richard Pracitto
- PET Center, Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Kyle C Wilcox
- Translational Imaging, AbbVie Inc, North Chicago, IL, 60064, USA
| | - Marcel Lindemann
- PET Center, Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Zachary Felchner
- PET Center, Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Li Zhang
- PET Center, Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Jie Tong
- PET Center, Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Krista Fowles
- PET Center, Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Sjoerd J Finnema
- Translational Imaging, AbbVie Inc, North Chicago, IL, 60064, USA
| | - Nabeel Nabulsi
- PET Center, Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Richard E Carson
- PET Center, Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Yiyun Huang
- PET Center, Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Zhengxin Cai
- PET Center, Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06520, USA.
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Zhao J, Mao Q, Lin F, Zhang B, Sun M, Zhang T, Wang S. Intramolecular hydrogen bond interruption and scaffold hopping of TMC-5 led to 2-(4-alkoxy-3-cyanophenyl)pyrimidine-4/5-carboxylic acids and 6-(4-alkoxy-3-cyanophenyl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-ones as potent pyrimidine-based xanthine oxidase inhibitors. Eur J Med Chem 2022; 229:114086. [PMID: 34992040 DOI: 10.1016/j.ejmech.2021.114086] [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: 11/23/2021] [Revised: 12/19/2021] [Accepted: 12/25/2021] [Indexed: 11/29/2022]
Abstract
Many pyrimidine-based xanthine oxidase (XO) inhibitors with diverse chemotypes have been reported recently. Our previous study revealed that 2-(4-alkoxy-3-cyano)phenyl-6-imino-1,6-dihydropyrimidine-5-carboxylic acid derivatives exhibited remarkable XO inhibitory potency. Notably, an intramolecular hydrogen bond (IMHB) formed between amino and carboxylic groups could be observed. With the hope to expand the structure-activity relationships (SARs) and obtain potential pyrimidine-based XO inhibitors, IMHB interruption and scaffold hopping were carried out on these compounds to design 2-(4-alkoxy-3-cyanophenyl)pyrimidine-4/5-carboxylic acids (11a-11n and 15a-15j) and 6-(4-alkoxy-3-cyanophenyl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-ones (19a-19j). Among them, compound 19a (IC50 = 0.039 μM) was identified as the most promising compound with substantially higher in vitro inhibitory potency than allopurinol (IC50 = 7.590 μM) and comparable to febuxostat (IC50 = 0.028 μM). The SAR analysis revealed that interrupting the IMHB through the removal of the amino group could damage the XO inhibitory potency; pyrimidine-4-carboxylic acid moiety was more beneficial for the XO inhibitory potency than the pyrimidine-5-carboxylic acid moiety. Additionally, enzyme kinetics studies suggested that compounds 11a, 15a and 19a acted as mixed-type inhibitors for XO and the removal of 6-position amino group resulted in a weakened affinity to the free enzyme, but an enhanced binding to the enzyme-substrate complex. Molecular modeling provided a reasonable explanation for the SARs observed in this study. Furthermore, in vivo hypouricemic effects demonstrated that compounds 15a and 19a could effectively reduce serum uric acid levels at an oral dose of 10 mg/kg, with 19a demonstrating a stronger effect than 15a. Therefore, our study proved that 6-(4-alkoxy-3-cyanophenyl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-ones were potent pyrimidine-based XO inhibitors and compound 19a required further structural optimization as a potential and efficacious agents for the treatment of hyperuricemia and gout.
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Affiliation(s)
- Jiaxing Zhao
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang 110016, China
| | - Qing Mao
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang 110016, China
| | - Fengwei Lin
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang 110016, China
| | - Bing Zhang
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang 110016, China
| | - Ming Sun
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang 110016, China
| | - Tingjian Zhang
- School of Pharmacy, China Medical University, 77 Puhe Road, North New Area, Shenyang, 110122, China.
| | - Shaojie Wang
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang 110016, China.
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Mourot L, Schmitt M, Mouray E, Spichty M, Florent I, Albrecht S. Structure-activity relationship and molecular modelling studies of quinazolinedione derivatives MMV665916 as potential antimalarial agent. Bioorg Med Chem 2021; 51:116513. [PMID: 34798379 DOI: 10.1016/j.bmc.2021.116513] [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: 06/23/2021] [Revised: 10/11/2021] [Accepted: 10/17/2021] [Indexed: 10/19/2022]
Abstract
A series of new quinazolinedione derivatives have been readily synthesized and evaluated for their in vitro antiplasmodial growth inhibition activity. Most of the compounds inhibited P. falciparum FcB1 strain in the low to medium micromolar concentration. The 2-ethoxy 8ag', 2-trifluoromethoxy 8ai' and 4-fluoro-2-methoxy 8ak' showed the best inhibitory activity with EC50 values around 5 µM and were non-toxic to the primary human fibroblast cell line AB943. However, these compounds were less potent than the original hit MMV665916, which showed remarkable growth inhibition with EC50 value of 0.4 µM and presented the highest selectivity index (SI > 250). In addition, a novel approach for determining the docking poses of these quinazolinedione derivatives with their potential protein target, the P. falciparum farnesyltransferase PfFT, was investigated.
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Affiliation(s)
- Laura Mourot
- Université de Haute-Alsace, Université de Strasbourg, CNRS, LIMA UMR 7042, F-68000 Mulhouse, France
| | - Marjorie Schmitt
- Université de Haute-Alsace, Université de Strasbourg, CNRS, LIMA UMR 7042, F-68000 Mulhouse, France
| | - Elisabeth Mouray
- Unité Molécules de Communication et Adaptation des Micro-organismes, UMR7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités, Paris, France
| | - Martin Spichty
- Université de Haute-Alsace, Université de Strasbourg, CNRS, LIMA UMR 7042, F-68000 Mulhouse, France
| | - Isabelle Florent
- Unité Molécules de Communication et Adaptation des Micro-organismes, UMR7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités, Paris, France
| | - Sébastien Albrecht
- Université de Haute-Alsace, Université de Strasbourg, CNRS, LIMA UMR 7042, F-68000 Mulhouse, France.
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García‐Marín J, Griera M, Alajarín R, Rodríguez‐Puyol M, Rodríguez‐Puyol D, Vaquero JJ. A Computer-Driven Scaffold-Hopping Approach Generating New PTP1B Inhibitors from the Pyrrolo[1,2-a]quinoxaline Core. ChemMedChem 2021; 16:2895-2906. [PMID: 34137509 PMCID: PMC8518816 DOI: 10.1002/cmdc.202100338] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/13/2021] [Indexed: 11/06/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a very promising target for the treatment of metabolic disorders such as type II diabetes mellitus. Although it was validated as a promising target for this disease more than 30 years ago, as yet there is no drug in advanced clinical trials, and its biochemical mechanism and functions are still being studied. In the present study, based on our experience generating PTP1B inhibitors, we have developed and implemented a scaffold-hopping approach to vary the pyrrole ring of the pyrrolo[1,2-a]quinoxaline core, supported by extensive computational techniques aimed to explain the molecular interaction with PTP1B. Using a combination of docking, molecular dynamics and end-point free-energy calculations, we have rationally designed a hypothesis for new PTP1B inhibitors, supporting their recognition mechanism at a molecular level. After the design phase, we were able to easily synthesize proposed candidates and their evaluation against PTP1B was found to be in good concordance with our predictions. Moreover, the best candidates exhibited glucose uptake increments in cellulo model, thus confirming their utility for PTP1B inhibition and validating this approach for inhibitors design and molecules thus obtained.
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Affiliation(s)
- Javier García‐Marín
- Departamento de Química Orgánica y Química InorgánicaUniversidad de Alcalá28805Alcalá de HenaresSpain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)Ctra. Colmenar Viejo, km. 910028034MadridSpain
- Instituto de Investigación Química Andrés Manuel del Río (IQAR)Universidad de AlcaláAlcalá de HenaresSpain
- Departamento de Química Biológica y EstructuralCentro de Investigaciones Biológicas Margarita Salas (CIB-CSIC)Calle Ramiro de Maeztu 928040MadridSpain
| | - Mercedes Griera
- Graphenano Medical Care, S.L.C/Pablo Casals, no. 13YeclaMurciaSpain
- Departamento de Biología de SistemasUniversidad de Alcalá28805Alcalá de HenaresSpain
| | - Ramón Alajarín
- Departamento de Química Orgánica y Química InorgánicaUniversidad de Alcalá28805Alcalá de HenaresSpain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)Ctra. Colmenar Viejo, km. 910028034MadridSpain
- Instituto de Investigación Química Andrés Manuel del Río (IQAR)Universidad de AlcaláAlcalá de HenaresSpain
| | - Manuel Rodríguez‐Puyol
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)Ctra. Colmenar Viejo, km. 910028034MadridSpain
- Departamento de Biología de SistemasUniversidad de Alcalá28805Alcalá de HenaresSpain
| | - Diego Rodríguez‐Puyol
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)Ctra. Colmenar Viejo, km. 910028034MadridSpain
- Fundación de Investigación BiomédicaUnidad de Nefrología del Hospital Príncipe de Asturias yDepartamento de Medicina y Especialidades MédicasUniversidad de Alcalá28805Alcalá de HenaresSpain
| | - Juan J. Vaquero
- Departamento de Química Orgánica y Química InorgánicaUniversidad de Alcalá28805Alcalá de HenaresSpain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)Ctra. Colmenar Viejo, km. 910028034MadridSpain
- Instituto de Investigación Química Andrés Manuel del Río (IQAR)Universidad de AlcaláAlcalá de HenaresSpain
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26
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Petrillo G, Tavani C, Bianchi L, Benzi A, Cavalluzzi MM, Salvagno L, Quintieri L, De Palma A, Caputo L, Rosato A, Lentini G. Densely Functionalized 2-Methylideneazetidines: Evaluation as Antibacterials. Molecules 2021; 26:3891. [PMID: 34202191 PMCID: PMC8271477 DOI: 10.3390/molecules26133891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 01/27/2023] Open
Abstract
Twenty-two novel, variously substituted nitroazetidines were designed as both sulfonamide and urethane vinylogs possibly endowed with antimicrobial activity. The compounds under study were obtained following a general procedure recently developed, starting from 4-nitropentadienoates deriving from a common β-nitrothiophenic precursor. While being devoid of any activity against fungi and Gram-negative bacteria, most of the title compounds performed as potent antibacterial agents on Gram-positive bacteria (E. faecalis and three strains of S. aureus), with the most potent congener being the 1-(4-chlorobenzyl)-3-nitro-4-(p-tolyl)azetidine 22, which displayed potency close to that of norfloxacin, the reference antibiotic (minimum inhibitory concentration values 4 and 1-2 μg/mL, respectively). Since 22 combines a relatively efficient activity against Gram-positive bacteria and a cytotoxicity on eucharyotic cells only at 4-times higher concentrations (inhibiting concentration on 50% of the cultured eukaryotic cells: 36 ± 10 μM, MIC: 8.6 μM), it may be considered as a promising hit compound for the development of a new series of antibacterials selectively active on Gram-positive pathogens. The relatively concise synthetic route described herein, based on widely available starting materials, could feed further structure-activity relationship studies, thus allowing for the fine investigation and optimization of the toxico-pharmacological profile.
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Affiliation(s)
- Giovanni Petrillo
- Department of Chemistry and Industrial Chemistry, University of Genoa, Via Dodecaneso 31, I-16146 Genoa, Italy; (C.T.); (L.B.); (A.B.)
| | - Cinzia Tavani
- Department of Chemistry and Industrial Chemistry, University of Genoa, Via Dodecaneso 31, I-16146 Genoa, Italy; (C.T.); (L.B.); (A.B.)
| | - Lara Bianchi
- Department of Chemistry and Industrial Chemistry, University of Genoa, Via Dodecaneso 31, I-16146 Genoa, Italy; (C.T.); (L.B.); (A.B.)
| | - Alice Benzi
- Department of Chemistry and Industrial Chemistry, University of Genoa, Via Dodecaneso 31, I-16146 Genoa, Italy; (C.T.); (L.B.); (A.B.)
| | - Maria Maddalena Cavalluzzi
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona n. 4, 70126 Bari, Italy; (M.M.C.); (L.S.); (A.R.); (G.L.)
| | - Lara Salvagno
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona n. 4, 70126 Bari, Italy; (M.M.C.); (L.S.); (A.R.); (G.L.)
| | - Laura Quintieri
- Institute of Sciences of Food Production (CNR-ISPA) National Council of Research, Via G. Amendola, 122/O, 70126 Bari, Italy; (L.Q.); (L.C.)
| | - Annalisa De Palma
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona 4, 70126 Bari, Italy;
| | - Leonardo Caputo
- Institute of Sciences of Food Production (CNR-ISPA) National Council of Research, Via G. Amendola, 122/O, 70126 Bari, Italy; (L.Q.); (L.C.)
| | - Antonio Rosato
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona n. 4, 70126 Bari, Italy; (M.M.C.); (L.S.); (A.R.); (G.L.)
| | - Giovanni Lentini
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona n. 4, 70126 Bari, Italy; (M.M.C.); (L.S.); (A.R.); (G.L.)
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Soltani S, Hallaj-Nezhadi S, Rashidi MR. A comprehensive review of in silico approaches for the prediction and modulation of aldehyde oxidase-mediated drug metabolism: The current features, challenges and future perspectives. Eur J Med Chem 2021; 222:113559. [PMID: 34119831 DOI: 10.1016/j.ejmech.2021.113559] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 01/09/2023]
Abstract
The importance of aldehyde oxidase (AOX) in drug metabolism necessitates the development and application of the in silico rational drug design methods as an integral part of drug discovery projects for the early prediction and modulation of AOX-mediated metabolism. The current study represents an up-to-date and thorough review of in silico studies of AOX-mediated metabolism and modulation methods. In addition, the challenges and the knowledge gap that should be covered have been discussed. The importance of aldehyde oxidase (AOX) in drug metabolism is a hot topic in drug discovery. Different strategies are available for the modulation of the AOX-mediated metabolism of drugs. Application of the rational drug design methods as an integral part of drug discovery projects is necessary for the early prediction of AOX-mediated metabolism. The current study represents a comprehensive review of AOX molecular structure, AOX-mediated reactions, AOX substrates, AOX inhibition, approaches to modify AOX-mediated metabolism, prediction of AOX metabolism/substrates/inhibitors, and the AOX related structure-activity relationship (SAR) studies. Furthermore, an up-to-date and thorough review of in silico studies of AOX metabolism has been carried out. In addition, the challenges and the knowledge gap that should be covered in the scientific literature have been discussed in the current review.
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Affiliation(s)
- Somaieh Soltani
- Pharmaceutical Analysis Research Center and Pharmacy Faculty, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Somayeh Hallaj-Nezhadi
- Drug Applied Research Center and Pharmacy Faculty, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Rashidi
- Stem Cell and Regenerative Medicine Institute and Pharmacy faculty, Tabriz University of Medical Sciences, Iran.
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28
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Pennington LD, Muegge I. Holistic drug design for multiparameter optimization in modern small molecule drug discovery. Bioorg Med Chem Lett 2021; 41:128003. [DOI: 10.1016/j.bmcl.2021.128003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 01/28/2023]
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Novel PF74-like small molecules targeting the HIV-1 capsid protein: Balance of potency and metabolic stability. Acta Pharm Sin B 2021; 11:810-822. [PMID: 33777683 PMCID: PMC7982424 DOI: 10.1016/j.apsb.2020.07.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/08/2020] [Accepted: 07/20/2020] [Indexed: 12/26/2022] Open
Abstract
Of all known small molecules targeting human immunodeficiency virus (HIV) capsid protein (CA), PF74 represents by far the best characterized chemotype, due to its ability to confer antiviral phenotypes in both early and late phases of viral replication. However, the prohibitively low metabolic stability renders PF74 a poor antiviral lead. We report herein our medicinal chemistry efforts toward identifying novel and metabolically stable small molecules targeting the PF74 binding site. Specifically, we replaced the inter-domain-interacting, electron-rich indole ring of PF74 with less electron-rich isosteres, including imidazolidine-2,4-dione, pyrimidine-2,4-dione, and benzamide, and identified four potent antiviral compounds (10, 19, 20 and 26) with markedly improved metabolic stability. Compared to PF74, analog 20 exhibited similar submicromolar potency, and much longer (51-fold) half-life in human liver microsomes (HLMs). Molecular docking corroborated that 20 binds to the PF74 binding site, and revealed distinct binding interactions conferred by the benzamide moiety. Collectively, our data support compound 20 as a promising antiviral lead.
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Key Words
- ART, antiretroviral therapy
- CA, capsid protein
- CACTD, CA C-terminal domain
- CANTD, CA N-terminal domain
- Capsid protein
- HBA, H-bond acceptor
- HBD, H-bond donor
- HIV, human immunodeficiency virus
- HIV-1
- HLM, human liver microsome
- MLM, mouse liver microsome
- Microsomal stability
- PF74
- PK, pharmacokinetic
- SAR, structure‒activity relationship
- TSA, thermal shift assay
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Mignani S, Majoral JP, Desaphy JF, Lentini G. From Riluzole to Dexpramipexole via Substituted-Benzothiazole Derivatives for Amyotrophic Lateral Sclerosis Disease Treatment: Case Studies. Molecules 2020; 25:E3320. [PMID: 32707914 PMCID: PMC7435757 DOI: 10.3390/molecules25153320] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022] Open
Abstract
The 1,3-benzothiazole (BTZ) ring may offer a valid option for scaffold-hopping from indole derivatives. Several BTZs have clinically relevant roles, mainly as CNS medicines and diagnostic agents, with riluzole being one of the most famous examples. Riluzole is currently the only approved drug to treat amyotrophic lateral sclerosis (ALS) but its efficacy is marginal. Several clinical studies have demonstrated only limited improvements in survival, without benefits to motor function in patients with ALS. Despite significant clinical trial efforts to understand the genetic, epigenetic, and molecular pathways linked to ALS pathophysiology, therapeutic translation has remained disappointingly slow, probably due to the complexity and the heterogeneity of this disease. Many other drugs to tackle ALS have been tested for 20 years without any success. Dexpramipexole is a BTZ structural analog of riluzole and was a great hope for the treatment of ALS. In this review, as an interesting case study in the development of a new medicine to treat ALS, we present the strategy of the development of dexpramipexole, which was one of the most promising drugs against ALS.
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Affiliation(s)
- Serge Mignani
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologique, Université Paris Descartes, PRES Sorbonne Paris Cité, CNRS UMR 860, 45, rue des Saints Peres, 75006 Paris, France
- CQM-Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - Jean-Pierre Majoral
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, 31077 Toulouse CEDEX 4, France;
- Université Toulouse, 118 route de Narbonne, 31077 Toulouse CEDEX 4, France
| | - Jean-François Desaphy
- Dipartimento di Scienze Biomediche e Oncologia Umana, Scuola di Medicina, Università degli Studi di Bari Aldo Moro, Piazza Giulio Cesare, 70124 Bari, Italy;
| | - Giovanni Lentini
- Dipartimento di Farmacia—Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona 4, 70125 Bari, Italy
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AboulWafa OM, Daabees HM, Badawi WA. 2-Anilinopyrimidine derivatives: Design, synthesis, in vitro anti-proliferative activity, EGFR and ARO inhibitory activity, cell cycle analysis and molecular docking study. Bioorg Chem 2020; 99:103798. [DOI: 10.1016/j.bioorg.2020.103798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/18/2020] [Accepted: 03/24/2020] [Indexed: 01/02/2023]
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