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Dong W, Zhang P. Predicting anti-trypanosome effect of carbazole-derived compounds by powerful SVM with novel kernel function and comprehensive learning PSO. Antimicrob Agents Chemother 2024; 68:e0026524. [PMID: 38808999 PMCID: PMC11232408 DOI: 10.1128/aac.00265-24] [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: 02/20/2024] [Accepted: 04/25/2024] [Indexed: 05/30/2024] Open
Abstract
In order to predict the anti-trypanosome effect of carbazole-derived compounds by quantitative structure-activity relationship, five models were established by the linear method, random forest, radial basis kernel function support vector machine, linear combination mix-kernel function support vector machine, and nonlinear combination mix-kernel function support vector machine (NLMIX-SVM). The heuristic method and optimized CatBoost were used to select two different key descriptor sets for building linear and nonlinear models, respectively. Hyperparameters in all nonlinear models were optimized by comprehensive learning particle swarm optimization with low complexity and fast convergence. Furthermore, the models' robustness and reliability underwent rigorous assessment using fivefold and leave-one-out cross-validation, y-randomization, and statistics including concordance correlation coefficient (CCC), [Formula: see text] , [Formula: see text] , and [Formula: see text] . Among all the models, the NLMIX-SVM model, which was established by support vector regression using a nonlinear combination of radial basis kernel function, sigmoid kernel function, and linear kernel function as a new kernel function, demonstrated excellent learning and generalization abilities as well as robustness: [Formula: see text] = 0.9581, mean square error (MSE) = 0.0199 for the training set and [Formula: see text] = 0.9528, MSE = 0.0174 for the test set. [Formula: see text] , [Formula: see text] , CCC, [Formula: see text] , [Formula: see text], and [Formula: see text] are 0.9539, 0.8908, 0.9752, 0.9529, 0.9528, and 0.9633, respectively. The NLMIX-SVM method proved to be a promising way in quantitative structure-activity relationship research. In addition, molecular docking experiments were conducted to analyze the properties of new derivatives, and a new potential candidate drug molecule was ultimately found. In summary, this study will provide help for the design and screening of novel anti-trypanosome drugs.
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Affiliation(s)
- Wenzhe Dong
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong Province, China
| | - Peijian Zhang
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong Province, China
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2
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Saganuwan SA. Structure-activity relationship of pharmacophores and toxicophores: the need for clinical strategy. Daru 2024:10.1007/s40199-024-00525-y. [PMID: 38935265 DOI: 10.1007/s40199-024-00525-y] [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: 11/20/2023] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
OBJECTIVES Sometimes clinical efficacy and potential risk of therapeutic and toxic agents are difficult to predict over a long period of time. Hence there is need for literature search with a view to assessing cause of toxicity and less efficacy of drugs used in clinical practice. METHOD Hence literatures were searched for physicochemical properties, chemical formulas, molecular masses, pH values, ionization, receptor type, agonist and antagonist, therapeutic, toxic and structure-activity relationship of chemical compounds with pharmacophore and toxicophore, with a view to identifying high efficacious and relative low toxic agents. Inclusion criteria were manuscripts published on PubMed, Scopus, Web of Science, PubMed Central, Google Scholar among others, between 1960 and 2023. Keywords such as pharmacophore, toxicophore, structure-activity-relationship and disease where also searched. The exclusion criteria were the chemicals that lack pharmacophore, toxicophore and manuscripts published before 1960. RESULTS Findings have shown that pharmacophore and toxicophore functional groups determine clinical efficacy and safety of therapeutics, but if they overlap therapeutic and toxicity effects go concurrently. Hence the functional groups, dose, co-administration and concentration of drugs at receptor, drug-receptor binding and duration of receptor binding are the determining factors of pharmacophore and toxicophore activity. Molecular mass, chemical configuration, pH value, receptor affinity and binding capacity, multiple pharmacophores, hydrophilic/lipophilic nature of the chemical contribute greatly to functionality of pharmacophore and toxicophore. CONCLUSION Daily single therapy, avoidance of reversible pharmacology, drugs with covalent adduct, maintenance of therapeutic dose, and the use of multiple pharmacophores for terminal diseases will minimize toxicity and improve efficacy.
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Affiliation(s)
- Saganuwan Alhaji Saganuwan
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Federal University of Agriculture, Makurdi, P.M.B. 2373, Benue State, Nigeria.
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3
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Amudala S, Sumit, Aidhen IS. LpxC inhibition: Potential and opportunities with carbohydrate scaffolds. Carbohydr Res 2024; 537:109057. [PMID: 38402732 DOI: 10.1016/j.carres.2024.109057] [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: 11/01/2023] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/27/2024]
Abstract
Uridine diphosphate-3-O-(hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a key enzyme involved in the biosynthesis of lipid A, an essential building block, for the construction and assembly of the outer membrane (OM) of Gram-negative bacteria. The enzyme is highly conserved in almost all Gram-negative bacteria and hence has emerged as a promising target for drug discovery in the fight against multi-drug resistant Gram-negative infections. Since the first nanomolar LpxC inhibitor, L-161,240, an oxazoline-based hydroxamate, the two-decade-long ongoing search has provided valuable information regarding essential features necessary for inhibition. Although the design and structure optimization for arriving at the most efficacious inhibitor of this enzyme has made good use of different heterocyclic moieties, the use of carbohydrate scaffold is scant. This review briefly covers the advancement and progress made in LpxC inhibition. The field awaits the use of potential associated with carbohydrate-based scaffolds for LpxC inhibition and the discovery of anti-bacterial agents against Gram-negative infections.
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Affiliation(s)
- Subramanyam Amudala
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India.
| | - Sumit
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Indrapal Singh Aidhen
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India.
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4
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Xue H, Zhang R, Yan X, Wang R, Zhang P. Study of PARP inhibitors for breast cancer based on enhanced multiple kernel function SVR with PSO. Front Pharmacol 2024; 15:1257253. [PMID: 38370471 PMCID: PMC10869605 DOI: 10.3389/fphar.2024.1257253] [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: 07/12/2023] [Accepted: 01/02/2024] [Indexed: 02/20/2024] Open
Abstract
PARP1 is one of six enzymes required for the highly error-prone DNA repair pathway microhomology-mediated end joining (MMEJ) and needs to be inhibited when over-expressed. In order to study the PARP1 inhibitory effect of fused tetracyclic or pentacyclic dihydrodiazepinoindolone derivatives (FTPDDs) by quantitative structure-activity relationship technique, six models were established by four kinds of methods, heuristic method, gene expression programming, random forester, and support vector regression with single, double, and triple kernel function respectively. The single, double, and triple kernel functions were RBF kernel function, the integration of RBF and polynomial kernel functions, and the integration of RBF, polynomial, and linear kernel functions respectively. The problem of multi-parameter optimization introduced in the support vector regression model was solved by the particle swarm optimization algorithm. Among the models, the model established by support vector regression with triple kernel function, in which the optimal R 2 and RMSE of training set and test set were 0.9353, 0.9348 and 0.0157, 0.0288, and R2 cv of training set and test set were 0.9090 and 0.8971, shows the strongest prediction ability and robustness. The method of support vector regression with triple kernel function is a great promotion in the field of quantitative structure-activity relationship, which will contribute a lot to designing and screening new drug molecules. The information contained in the model can provide important factors that guide drug design. Based on these factors, six new FTPDDs have been designed. Using molecular docking experiments to determine the properties of new derivatives, the new drug was ultimately successfully designed.
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Affiliation(s)
| | | | | | | | - Peijian Zhang
- University, College of Computer Science and Technology, Qingdao, China
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5
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Choi K. Structure-property Relationships Reported for the New Drugs Approved in 2022. Mini Rev Med Chem 2024; 24:330-340. [PMID: 37211842 DOI: 10.2174/1389557523666230519162803] [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: 01/20/2023] [Revised: 02/20/2023] [Accepted: 03/15/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND The structure-property relationship illustrates how modifying the chemical structure of a pharmaceutical compound influences its absorption, distribution, metabolism, excretion, and other related properties. Understanding structure-property relationships of clinically approved drugs could provide useful information for drug design and optimization strategies. METHOD Among new drugs approved around the world in 2022, including 37 in the US, structure- property relationships of seven drugs were compiled from medicinal chemistry literature, in which detailed pharmacokinetic and/or physicochemical properties were disclosed not only for the final drug but also for its key analogues generated during drug development. RESULTS The discovery campaigns for these seven drugs demonstrate extensive design and optimization efforts to identify suitable candidates for clinical development. Several strategies have been successfully employed, such as attaching a solubilizing group, bioisosteric replacement, and deuterium incorporation, resulting in new compounds with enhanced physicochemical and pharmacokinetic properties. CONCLUSION The structure-property relationships hereby summarized illustrate how proper structural modifications could successfully improve the overall drug-like properties. The structure-property relationships of clinically approved drugs are expected to continue to provide valuable references and guides for the development of future drugs.
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Affiliation(s)
- Kihang Choi
- Department of Chemistry, Korea University, Seoul, 02841, Korea (ROK)
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6
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Papa A, Cursaro I, Pozzetti L, Contri C, Cappello M, Pasquini S, Carullo G, Ramunno A, Gemma S, Varani K, Butini S, Campiani G, Vincenzi F. Pioneering first-in-class FAAH-HDAC inhibitors as potential multitarget neuroprotective agents. Arch Pharm (Weinheim) 2023; 356:e2300410. [PMID: 37750286 DOI: 10.1002/ardp.202300410] [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: 07/28/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 09/27/2023]
Abstract
Aiming to simultaneously modulate the endocannabinoid system (ECS) functions and the epigenetic machinery, we selected the fatty acid amide hydrolase (FAAH) and histone deacetylase (HDAC) enzymes as desired targets to develop potential neuroprotective multitarget-directed ligands (MTDLs), expecting to achieve an additive or synergistic therapeutic effect in oxidative stress-related conditions. We herein report the design, synthesis, and biological evaluation of the first-in-class FAAH-HDAC multitarget inhibitors. A pharmacophore merging strategy was applied, yielding 1-phenylpyrrole-based compounds 4a-j. The best-performing compounds (4c, 4f, and 4h) were tested for their neuroprotective properties in oxidative stress models, employing 1321N1 human astrocytoma cells and SHSY5 human neuronal cells. In our preliminary studies, compound 4h stood out, showing a balanced nanomolar inhibitory activity against the selected targets and outperforming the standard antioxidant N-acetylcysteine in vitro. Together with 4f, 4h was also able to protect 1321N1 cells from tert-butyl hydroperoxide or glutamate insult. Our study may provide the basis for the development of novel MTDLs targeting the ECS and epigenetic enzymes.
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Affiliation(s)
- Alessandro Papa
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Ilaria Cursaro
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Luca Pozzetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Chiara Contri
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Martina Cappello
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Silvia Pasquini
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Gabriele Carullo
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Anna Ramunno
- Department of Pharmacy, University of Salerno, Fisciano, Italy
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Katia Varani
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Fabrizio Vincenzi
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
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Song F, Sun H, Ma X, Wang W, Luan M, Zhai H, Su G, Liu Y. QSAR and molecular docking studies on designing potent inhibitors of SARS-CoVs main protease. Front Pharmacol 2023; 14:1185004. [PMID: 37266150 PMCID: PMC10230167 DOI: 10.3389/fphar.2023.1185004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/18/2023] [Indexed: 06/03/2023] Open
Abstract
Background: Severe acute respiratory syndrome coronavirus (SARS-CoVs) have emerged as a global health threat, which had caused a high rate of mortality. There is an urgent need to find effective drugs against these viruses. Objective: This study aims to predict the activity of unsymmetrical aromatic disulfides by constructing a QSAR model, and to design new compounds according to the structural and physicochemical attributes responsible for higher activity towards SARS-CoVs main protease. Methods: All molecules were constructed in ChemOffice software and molecular descriptors were calculated by CODESSA software. A regression-based linear heuristic method was established by changing descriptors datasets and calculating predicted IC50 values of compounds. Then, some new compounds were designed according to molecular descriptors from the heuristic method model. The compounds with predicted values smaller than a set point were constantly screened out. Finally, the properties analysis and molecular docking were conducted to further understand the structure-activity relationships of these finalized compounds. Results: The heuristic method explored the various descriptors responsible for bioactivity and gained the best linear model with R2 0.87. The success of the model fully passed the testing set validation, proving that the model has both high statistical significance and excellent predictive ability. A total of 5 compounds with ideal predicted IC50 were found from the 96 newly designed derivatives and their properties analyze was carried out. Molecular docking experiments were conducted for the optimal compound 31a, which has the best compound activity with good target protein binding capability. Conclusion: The heuristic method was quite reliable for predicting IC50 values of unsymmetrical aromatic disulfides. The present research provides meaningful guidance for further exploration of the highly active inhibitors for SARS-CoVs.
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Affiliation(s)
- Fucheng Song
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China
| | - Haoyang Sun
- Department of Traditional Chinese Medicine, Songshan Hospital of Qingdao University, Qingdao, China
| | - Xiaofang Ma
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China
| | - Wei Wang
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China
| | | | - Honglin Zhai
- Department of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Guanmin Su
- Shandong Provincial Center for Disease Control and Prevention, Jinan, China
| | - Yantao Liu
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China
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8
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Tamaian R, Porozov Y, Shityakov S. Exhaustive in silico design and screening of novel antipsychotic compounds with improved pharmacodynamics and blood-brain barrier permeation properties. J Biomol Struct Dyn 2023; 41:14849-14870. [PMID: 36927517 DOI: 10.1080/07391102.2023.2184179] [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: 09/15/2022] [Accepted: 02/18/2023] [Indexed: 03/18/2023]
Abstract
Antipsychotic drugs or neuroleptics are widely used in the treatment of psychosis as a manifestation of schizophrenia and bipolar disorder. However, their effectiveness largely depends on the blood-brain barrier (BBB) permeation (pharmacokinetics) and drug-receptor pharmacodynamics. Therefore, in this study, we developed and implemented the in silico pipeline to design novel compounds (n = 260) as leads using the standard drug scaffolds with improved PK/PD properties from the standard scaffolds. As a result, the best candidates (n = 3) were evaluated in molecular docking to interact with serotonin and dopamine receptors. Finally, haloperidol (HAL) derivative (1-(4-fluorophenyl)-4-(4-hydroxy-4-{4-[(2-phenyl-1,3-thiazol-4-yl)methyl]phenyl}piperidin-1-yl)butan-1-one) was identified as a "magic shotgun" lead compound with better affinity to the 5-HT2A, 5-HT1D, D2, D3, and 5-HT1B receptors than the control molecule. Additionally, this hit substance was predicted to possess similar BBB permeation properties and much lower toxicological profiles in comparison to HAL. Overall, the proposed rational drug design platform for novel antipsychotic drugs based on the BBB permeation and receptor binding might be an invaluable asset for a medicinal chemist or translational pharmacologist.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Radu Tamaian
- ICSI Analytics, National Research and Development Institute for Cryogenics and Isotopic Technologies - ICSI Rm. Vâlcea, Râmnicu Vâlcea, Romania
| | - Yuri Porozov
- Center of Bio- and Chemoinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint-Petersburg, Russia
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9
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Abate C, Decherchi S, Cavalli A. Graph neural networks for conditional de novo drug design. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Carlo Abate
- Fondazione Istituto Italiano di Tecnologia Genoa Italy
- Università degli Studi di Bologna Bologna Italy
| | | | - Andrea Cavalli
- Fondazione Istituto Italiano di Tecnologia Genoa Italy
- Università degli Studi di Bologna Bologna Italy
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10
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Romero AH, Aguilera E, Gotopo L, Charris J, Rodríguez N, Oviedo H, Dávila B, Cabrera G, Cerecetto H. Synthesis and Antitrypanosomal and Mechanistic Studies of a Series of 2-Arylquinazolin-4-hydrazines: A Hydrazine Moiety as a Selective, Safe, and Specific Pharmacophore to Design Antitrypanosomal Agents Targeting NO Release. ACS OMEGA 2022; 7:47225-47238. [PMID: 36570252 PMCID: PMC9773939 DOI: 10.1021/acsomega.2c06455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Nitric oxide (NO) represents a valuable target to design antitrypanosomal agents by its high toxicity against trypanosomatids and minimal side effects on host macrophages. The progress of NO-donors as antitrypanosomal has been restricted by the high toxicity of their agents, which usually is based on NO-heterocycles and metallic NO-complexes. Herein, we carried out the design of a new class of NO-donors based on the susceptibility of the hydrazine moiety connected to an electron-deficient ring to be reduced to the amine moiety with release of NO. Then, a series of novel 2-arylquinazolin-4-hydrazine, with the potential ability to disrupt the parasite folate metabolism, were synthesized. Their in vitro evaluation against Leishmania and Trypanosoma cruzi parasites and mechanistic aspects were investigated. The compounds displayed significant leishmanicidal activity, identifying three potential candidates, that is, 3b, 3c, and 3f, for further assays by their good antiamastigote activities against Leishmania braziliensis, low toxicity, non-mutagenicity, and good ADME profile. Against T. cruzi parasites, derivatives 3b, 3c, and 3e displayed interesting levels of activities and selectivities. Mechanistic studies revealed that the 2-arylquinazolin-4-hydrazines act as either antifolate or NO-donor agents. NMR, fluorescence, and theoretical studies supported the fact that the quinazolin-hydrazine decomposed easily in an oxidative environment via cleavage of the N-N bond to release the corresponding heterocyclic-amine and NO. Generation of NO from axenic parasites was confirmed by the Griess test. All the evidence showed the potential of hydrazine connected to the electron-deficient ring to design effective and safe NO-donors against trypanosomatids.
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Affiliation(s)
- Angel H. Romero
- Grupo
de Química Orgánica Medicinal, Instituto de Química
Biológica, Facultad de Ciencias, Universidad de la Republica, Iguá 4225, Montevideo 11400, Uruguay
- Laboratorio
de Ingeniería Genética, Instituto de Biomedicina, Facultad
de Medicina, Universidad Central de Venezuela, San Luis, Caracas 1073, Venezuela
| | - Elena Aguilera
- Grupo
de Química Orgánica Medicinal, Instituto de Química
Biológica, Facultad de Ciencias, Universidad de la Republica, Iguá 4225, Montevideo 11400, Uruguay
| | - Lourdes Gotopo
- Laboratorio
de Síntesis de Orgánica, Facultad de Ciencias, Universidad Central de Venezuela, Los Chaguaramos, Caracas 1041-A, Venezuela
| | - Jaime Charris
- Laboratorio
de Síntesis de Medicamentos, Facultad de Farmacia, Universidad Central de Venezuela, Los Chaguaramos, Caracas 1041-A, Venezuela
| | - Noris Rodríguez
- Laboratorio
de Ingeniería Genética, Instituto de Biomedicina, Facultad
de Medicina, Universidad Central de Venezuela, San Luis, Caracas 1073, Venezuela
| | - Henry Oviedo
- Laboratorio
de Ingeniería Genética, Instituto de Biomedicina, Facultad
de Medicina, Universidad Central de Venezuela, San Luis, Caracas 1073, Venezuela
| | - Belén Dávila
- Grupo
de Química Orgánica Medicinal, Instituto de Química
Biológica, Facultad de Ciencias, Universidad de la Republica, Iguá 4225, Montevideo 11400, Uruguay
| | - Gustavo Cabrera
- Laboratorio
de Síntesis de Orgánica, Facultad de Ciencias, Universidad Central de Venezuela, Los Chaguaramos, Caracas 1041-A, Venezuela
| | - Hugo Cerecetto
- Grupo
de Química Orgánica Medicinal, Instituto de Química
Biológica, Facultad de Ciencias, Universidad de la Republica, Iguá 4225, Montevideo 11400, Uruguay
- Área
de Radiofarmacia, Centro de Investigaciones Nucleares, Facultad de
Ciencias, Universidad de la Republica, Mataojo 2055, Montevideo 11400, Uruguay
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11
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Georgiev T, Hadzhibozheva P, Karamalakova Y, Georgieva E, Perinkadakatt F, Ilinov Z, Petkov K, Ananiev J. Therapeutic approach of glutathione/glutathione peroxidase-4 axis modulation in the light of ferroptosis. PHARMACIA 2022. [DOI: 10.3897/pharmacia.69.e87716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In the 21st century beginning, the evidence of a new type of programmed cell death, different from apoptosis, began to accumulate. In 2012, the ferroptosis concept was officially introduced. It refers to a kind of cell death that is associated with iron accumulation in the cell, impaired redox potential, and ROS increment with concomitant lipid peroxidation. Ferroptosis plays an important role in the pathophysiology of several organ damages such as tumors, neurodegenerative, ischemia-reperfusion, inflammatory diseases, and others. In ferroptosis, the leading mechanism is the glutathione (GSH) depletion and inactivation of Glutathione peroxidase-4 (GPX4), which strongly shifts the oxidative balance in the cell, leading to the activation of certain signalling pathways to induce oxidative death. The article aims to focus attention on the modulation of the GSH/GPX axis as a key factor in the treatment of these diseases.
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Manasa G, Bhakta AK, Bafna J, Mascarenhas RJ, Malode SJ, Shetti NP. An amperometric sensor composed of carbon hybrid-structure for the degradation of aminotriazole herbicide. ENVIRONMENTAL RESEARCH 2022; 212:113541. [PMID: 35640708 DOI: 10.1016/j.envres.2022.113541] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/20/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The use of the herbicide aminotriazole (3-ATA) in agriculture poses rising concerns about global water-borne contamination. Due to its toxicity which is known to cause cancer and thyroid dysfunction, 3-ATA is considered an important analytical target. Environmental protection agencies worldwide have introduced several directives that set concentration limits for chemicals to combat water pollution. Hence, to evaluate the presence of 3-ATA in water and limit their impact on ecosystems and human health, the development of an efficient real-time monitoring device is the key. The as-synthesized copper oxide decorated multiwall carbon nanotubes at 400 °C (CuO-MWCNT@400) showed remarkable efficiency as modifiers. Under optimal conditions, we explored the direct oxidation of 3-ATA at CuO-MWCNT@400 modified carbon paste electrode (MCPE). With its distinguishing synergistic features like high levels of porosity, stability, and surface area, this structure favoured greater detection, selectivity, and sensitivity. The amperometric i-t curve technique was adopted for the first time for 3-ATA quantification. This technique rendered a good detection sensitivity of 1.65 × 10-8 mol L-1 and anti-interference characteristics for several interferent species, including fungicides, fertilizers, herbicides, inorganic ions, and carbohydrates. Finally, the proof-of-concept was yielded by selective and sensitive detection of 3-ATA from two different samples of spiked water. We believe this work will enhance awareness and garner appreciation of the electrochemical sensor's analytical performance in protecting our environment and water resources.
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Affiliation(s)
- G Manasa
- Electrochemistry Research Group, Department of Chemistry, St. Joseph's College (Autonomous), Lalbagh Road, Bangalore, 560027, Karnataka, India
| | - Arvind K Bhakta
- Electrochemistry Research Group, Department of Chemistry, St. Joseph's College (Autonomous), Lalbagh Road, Bangalore, 560027, Karnataka, India
| | - Jeevika Bafna
- Electrochemistry Research Group, Department of Chemistry, St. Joseph's College (Autonomous), Lalbagh Road, Bangalore, 560027, Karnataka, India
| | - Ronald J Mascarenhas
- Electrochemistry Research Group, Department of Chemistry, St. Joseph's College (Autonomous), Lalbagh Road, Bangalore, 560027, Karnataka, India.
| | - Shweta J Malode
- Department of Chemistry, School of Advanced Sciences, KLE Technological University, Vidyanagar, Hubballi, 580 031, Karnataka, India
| | - Nagaraj P Shetti
- Department of Chemistry, School of Advanced Sciences, KLE Technological University, Vidyanagar, Hubballi, 580 031, Karnataka, India.
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13
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Male contraceptive development: A medicinal chemistry perspective. Eur J Med Chem 2022; 243:114709. [DOI: 10.1016/j.ejmech.2022.114709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/20/2022] [Accepted: 08/21/2022] [Indexed: 11/21/2022]
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14
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Improving Antimicrobial Activity and Physico-Chemical Properties by Isosteric Replacement of 2-Aminothiazole with 2-Aminooxazole. Pharmaceuticals (Basel) 2022; 15:ph15050580. [PMID: 35631406 PMCID: PMC9143880 DOI: 10.3390/ph15050580] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 02/01/2023] Open
Abstract
Antimicrobial drug resistance is currently one of the most critical health issues. Pathogens resistant to last-resort antibiotics are increasing, and very few effective antibacterial agents have been introduced in recent years. The promising drug candidates are often discontinued in the primary stages of the drug discovery pipeline due to their unspecific reactivity (PAINS), toxicity, insufficient stability, or low water solubility. In this work, we investigated a series of substituted N-oxazolyl- and N-thiazolylcarboxamides of various pyridinecarboxylic acids. Final compounds were tested against several microbial species. In general, oxazole-containing compounds showed high activity against mycobacteria, especially Mycobacterium tuberculosis (best MICH37Ra = 3.13 µg/mL), including the multidrug-resistant strains. Promising activities against various bacterial and fungal strains were also observed. None of the compounds was significantly cytotoxic against the HepG2 cell line. Experimental measurement of lipophilicity parameter log k’w and water solubility (log S) confirmed significantly (typically two orders in logarithmic scale) increased hydrophilicity/water solubility of oxazole derivatives in comparison with their thiazole isosteres. Mycobacterial β-ketoacyl-acyl carrier protein synthase III (FabH) was suggested as a probable target by molecular docking and molecular dynamics simulations.
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15
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Khalil F, Onyango JO. Effect of Patent Expiry on the Performance of Innovator Multinational Pharmaceutical Companies in a Low Middle Income Country. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 4:783460. [PMID: 35445207 PMCID: PMC9014174 DOI: 10.3389/fmedt.2022.783460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 02/21/2022] [Indexed: 11/19/2022] Open
Abstract
Patent expiry or loss of exclusivity exposes innovator pharmaceutical companies to changes in the market dynamics brought about by increased production of generics by rival companies after patent expiration. This current study focused on the effect of generic products manufacturing and competitive market pressures, price changes, and changes in sales volumes and profitability of innovator multinational pharmaceutical companies after patent expiry. The methodology of this study involved a descriptive survey design and utilized both qualitative and quantitative techniques for data collection, analysis, and presentation. Primary data were collected using the key informants' in-depth interviews and survey questionnaires. The top management, including regional managers, general managers, and directors of each of the eight companies participating in this study, were interviewed to gather the qualitative data. Thirty-six respondents comprising of Product Development Managers and Business Supervising Managers responded to a survey questionnaire through purposive sampling. Findings depicted a significant effect of patent expiry on the generic production and subsequent decline in the performance of multinational innovator companies in the pharmaceutical industry. This study recommends that multinational innovator companies operating in low-income countries, such as Kenya, develop strategic policies to tap into the market by leveraging generic production through collaborative manufacturing with generic companies to share revenues.
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Affiliation(s)
| | - Joseph Odhiambo Onyango
- Strathmore Business School, Institute of Healthcare Management, Strathmore University, Nairobi, Kenya
- Strathmore Business School, Strathmore University, Nairobi, Kenya
- *Correspondence: Joseph Odhiambo Onyango
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16
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Yu X, Li S, Zhu X, Kong Y. Inhibitors of protease activated receptor 4 (PAR4): a review of recent patents (2013-2021). Expert Opin Ther Pat 2022; 32:153-170. [PMID: 35081321 DOI: 10.1080/13543776.2022.2034786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Protease-activated receptor 4 (PAR4), belonging to a subfamily of G-protein-coupled receptors (GPCR), is expressed on the surface of Human platelets, and the activation of it can lead to platelets aggregation. Studies demonstrated that PAR4 inhibition protect mice from arterial/arteriolar thrombosis, pulmonary embolism and cerebral infarct, while do not affect the haemostatic responses integrity. Therefore, PAR4 has been a promising target for the development of anti-thrombotic agents. AREAS COVERED This review covers recent patents and literature on PAR4 and their application published between 2013 and 2021. EXPERT OPINION PAR4 is a promising anti-thrombotic target and PAR4 inhibitors are important biologically active compounds for the treatment of thrombosis. Most the recent patents and literature focus on PAR4 selective inhibitors, and BMS-986120 and BMS-986141, which were developed by BMS, have entered clinical trials. With the deep understanding of the crystal structures and biological functions of PAR4, we believe that many other novel types of molecules targeting PAR4 would enter the clinical studies or the market.
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Affiliation(s)
- Xiangying Yu
- School of Life & Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Shanshan Li
- Institute of Medicinal & Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Xiong Zhu
- Institute of Medicinal & Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yi Kong
- School of Life & Technology, China Pharmaceutical University, Nanjing, 210009, PR China
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17
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Cushman M. Design and Synthesis of Indenoisoquinolines Targeting Topoisomerase I and Other Biological Macromolecules for Cancer Chemotherapy. J Med Chem 2021; 64:17572-17600. [PMID: 34879200 DOI: 10.1021/acs.jmedchem.1c01491] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The discovery that certain indenoisoquinolines inhibit the religation reaction of DNA in the topoisomerase I-DNA-indenoisoquinoline ternary complex led to a structure-based drug design research program which resulted in three representatives that entered Phase I clinical trials in cancer patients at the National Cancer Institute. This has stimulated a great deal of interest in the design and execution of new synthetic pathways for indenoisoquinoline production. More recently, modulation of the substitution pattern and chemical nature of substituents on the indenoisoquinoline scaffold has resulted in a widening scope of additional biological targets, including RXR, PARP-1, MYC promoter G-quadruplex, topoisomerase II, estrogen receptor, VEGFR-2, HIF-1α, and tyrosyl DNA phosphodiesterases 1 and 2. Furthermore, convincing evidence has been advanced supporting the potential use of indenoisoquinolines for the treatment of diseases other than cancer. The rapidly expanding indenoisoquinoline knowledge base has provided a firm foundation for further advancements in indenoisoquinoline chemistry, pharmacology, and therapeutics.
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Affiliation(s)
- Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
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18
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Pal R, Singh K, Khan SA, Chawla P, Kumar B, Akhtar MJ. Reactive metabolites of the anticonvulsant drugs and approaches to minimize the adverse drug reaction. Eur J Med Chem 2021; 226:113890. [PMID: 34628237 DOI: 10.1016/j.ejmech.2021.113890] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/01/2021] [Accepted: 09/29/2021] [Indexed: 12/22/2022]
Abstract
Several generations of antiepileptic drugs (AEDs) are available in the market for the treatment of seizures, but these are amalgamated with acute to chronic side effects. The most common side effects of AEDs are dose-related, but some are idiosyncratic adverse drug reactions (ADRs) that transpire due to the formation of reactive metabolite (RM) after the bioactivation process. Because of the adverse reactions patients usually discontinue the medication in between the treatment. The AEDs such as valproic acid, lamotrigine, phenytoin etc., can be categorized under such types because they form the RM which may prevail with life-threatening adverse effects or immune-mediated reactions. Hepatotoxicity, teratogenicity, cutaneous hypersensitivity, dizziness, addiction, serum sickness reaction, renal calculi, metabolic acidosis are associated with the metabolites of drugs such as arene oxide, N-desmethyldiazepam, 2-(1-hydroxyethyl)-2-methylsuccinimide, 2-(sulphamoy1acetyl)-phenol, E-2-en-VPA and 4-en-VPA and carbamazepine-10,11-epoxide, etc. The major toxicities are associated with the moieties that are either capable of forming RM or the functional groups may itself be too reactive prior to the metabolism. These functional groups or fragment structures are typically known as structural alerts or toxicophores. Therefore, minimizing the bioactivation potential of lead structures in the early phases of drug discovery by a modification to low-risk drug molecules is a priority for the pharmaceutical companies. Additionally, excellent potency and pharmacokinetic (PK) behaviour help in ensuring that appropriate (low dose) candidate drugs progress into the development phase. The current review discusses about RMs in the anticonvulsant drugs along with their mechanism vis-a-vis research efforts that have been taken to minimize the toxic effects of AEDs therapy.
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Affiliation(s)
- Rohit Pal
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, Ferozpur, G.T. Road, Moga, 142001, Punjab, India
| | - Karanvir Singh
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, Ferozpur, G.T. Road, Moga, 142001, Punjab, India
| | - Shah Alam Khan
- Department of Pharmaceutical Chemistry, College of Pharmacy, National University of Science and Technology, PO 620, PC 130, Azaiba, Bousher, Muscat, Oman
| | - Pooja Chawla
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, Ferozpur, G.T. Road, Moga, 142001, Punjab, India
| | - Bhupinder Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, Ferozpur, G.T. Road, Moga, 142001, Punjab, India.
| | - Md Jawaid Akhtar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, Ferozpur, G.T. Road, Moga, 142001, Punjab, India; Department of Pharmaceutical Chemistry, College of Pharmacy, National University of Science and Technology, PO 620, PC 130, Azaiba, Bousher, Muscat, Oman.
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19
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Artificial Intelligence in Drug Safety and Metabolism. Methods Mol Biol 2021; 2390:483-501. [PMID: 34731484 DOI: 10.1007/978-1-0716-1787-8_22] [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: 05/14/2023]
Abstract
The use of artificial intelligence methods in drug safety began in the early 2000s with applications such as predicting bacterial mutagenicity and hERG inhibition. The field has been endlessly expanding ever since and the models have become more complex. These approaches are now integrated into molecule risk assessment processes along with in vitro and in vivo methods. Today, artificial intelligence can be used in every phase of drug discovery and development, from profiling chemical libraries in early discovery, to predicting off-target effects in the mid-discovery phase, to assessing potential mutagenic impurities in development and degradants as part of life cycle management. This chapter provides an overview of artificial intelligence in drug safety and describes its application throughout the entire discovery and development process.
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20
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Van Manh N, Hoang VH, Ngo VTH, Ann J, Jang TH, Ha JH, Song JY, Ha HJ, Kim H, Kim YH, Lee J, Lee J. Discovery of highly potent human glutaminyl cyclase (QC) inhibitors as anti-Alzheimer's agents by the combination of pharmacophore-based and structure-based design. Eur J Med Chem 2021; 226:113819. [PMID: 34536669 DOI: 10.1016/j.ejmech.2021.113819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022]
Abstract
The inhibition of glutaminyl cyclase (QC) may provide a promising strategy for the treatment of early Alzheimer's disease (AD) by reducing the amount of the toxic pyroform of β-amyloid (AβΝ3pE) in the brains of AD patients. In this work, we identified potent QC inhibitors with subnanomolar IC50 values that were up to 290-fold higher than that of PQ912, which is currently being tested in Phase II clinical trials. Among the tested compounds, the cyclopentylmethyl derivative (214) exhibited the most potent in vitro activity (IC50 = 0.1 nM), while benzimidazole (227) showed the most promising in vivo efficacy, selectivity and druggable profile. 227 significantly reduced the concentration of pyroform Aβ and total Aβ in the brain of an AD animal model and improved the alternation behavior of mice during Y-maze tests. The crystal structure of human QC (hQC) in complex with 214 indicated tight binding at the active site, supporting that the specific inhibition of QC results in potent in vitro and in vivo activity. Considering the recent clinical success of donanemab, which targets AβΝ3pE, small molecule-based QC inhibitors may also provide potential therapeutic options for early-stage AD treatment.
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Affiliation(s)
- Nguyen Van Manh
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Van-Hai Hoang
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Van T H Ngo
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea; Graduate Department of Healthcare Science, Dainam University, Hanoi, Viet Nam
| | - Jihyae Ann
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Tae-Ho Jang
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea
| | - Jung-Hye Ha
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea
| | - Jae Young Song
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea
| | - Hee-Jin Ha
- Medifron DBT, Seoul, 08502, Republic of Korea
| | - Hee Kim
- Medifron DBT, Seoul, 08502, Republic of Korea
| | | | - Jiyoun Lee
- Department of Global Medical Science, Sungshin University, Seoul, 01133, Republic of Korea
| | - Jeewoo Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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21
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Metz A, Wollenhaupt J, Glöckner S, Messini N, Huber S, Barthel T, Merabet A, Gerber HD, Heine A, Klebe G, Weiss MS. Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking. Acta Crystallogr D Struct Biol 2021; 77:1168-1182. [PMID: 34473087 PMCID: PMC8411975 DOI: 10.1107/s2059798321008196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/09/2021] [Indexed: 11/10/2022] Open
Abstract
In recent years, crystallographic fragment screening has matured into an almost routine experiment at several modern synchrotron sites. The hits of the screening experiment, i.e. small molecules or fragments binding to the target protein, are revealed along with their 3D structural information. Therefore, they can serve as useful starting points for further structure-based hit-to-lead development. However, the progression of fragment hits to tool compounds or even leads is often hampered by a lack of chemical feasibility. As an attractive alternative, compound analogs that embed the fragment hit structurally may be obtained from commercial catalogs. Here, a workflow is reported based on filtering and assessing such potential follow-up compounds by template docking. This means that the crystallographic binding pose was integrated into the docking calculations as a central starting parameter. Subsequently, the candidates are scored on their interactions within the binding pocket. In an initial proof-of-concept study using five starting fragments known to bind to the aspartic protease endothiapepsin, 28 follow-up compounds were selected using the designed workflow and their binding was assessed by crystallography. Ten of these compounds bound to the active site and five of them showed significantly increased affinity in isothermal titration calorimetry of up to single-digit micromolar affinity. Taken together, this strategy is capable of efficiently evolving the initial fragment hits without major synthesis efforts and with full control by X-ray crystallography.
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Affiliation(s)
- Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Steffen Glöckner
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Niki Messini
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Simon Huber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Ahmed Merabet
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Hans-Dieter Gerber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
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22
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Flynn NR, Ward MD, Schleiff MA, Laurin CMC, Farmer R, Conway SJ, Boysen G, Swamidass SJ, Miller GP. Bioactivation of Isoxazole-Containing Bromodomain and Extra-Terminal Domain (BET) Inhibitors. Metabolites 2021; 11:metabo11060390. [PMID: 34203690 PMCID: PMC8232216 DOI: 10.3390/metabo11060390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 12/15/2022] Open
Abstract
The 3,5-dimethylisoxazole motif has become a useful and popular acetyl-lysine mimic employed in isoxazole-containing bromodomain and extra-terminal (BET) inhibitors but may introduce the potential for bioactivations into toxic reactive metabolites. As a test, we coupled deep neural models for quinone formation, metabolite structures, and biomolecule reactivity to predict bioactivation pathways for 32 BET inhibitors and validate the bioactivation of select inhibitors experimentally. Based on model predictions, inhibitors were more likely to undergo bioactivation than reported non-bioactivated molecules containing isoxazoles. The model outputs varied with substituents indicating the ability to scale their impact on bioactivation. We selected OXFBD02, OXFBD04, and I-BET151 for more in-depth analysis. OXFBD’s bioactivations were evenly split between traditional quinones and novel extended quinone-methides involving the isoxazole yet strongly favored the latter quinones. Subsequent experimental studies confirmed the formation of both types of quinones for OXFBD molecules, yet traditional quinones were the dominant reactive metabolites. Modeled I-BET151 bioactivations led to extended quinone-methides, which were not verified experimentally. The differences in observed and predicted bioactivations reflected the need to improve overall bioactivation scaling. Nevertheless, our coupled modeling approach predicted BET inhibitor bioactivations including novel extended quinone methides, and we experimentally verified those pathways highlighting potential concerns for toxicity in the development of these new drug leads.
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Affiliation(s)
- Noah R. Flynn
- Department of Pathology and Immunology, Washington University-St. Louis, St. Louis, MO 63130, USA; (N.R.F.); (M.D.W.); (R.F.)
| | - Michael D. Ward
- Department of Pathology and Immunology, Washington University-St. Louis, St. Louis, MO 63130, USA; (N.R.F.); (M.D.W.); (R.F.)
| | - Mary A. Schleiff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | | | - Rohit Farmer
- Department of Pathology and Immunology, Washington University-St. Louis, St. Louis, MO 63130, USA; (N.R.F.); (M.D.W.); (R.F.)
| | - Stuart J. Conway
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; (C.M.C.L.); (S.J.C.)
| | - Gunnar Boysen
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - S. Joshua Swamidass
- Department of Pathology and Immunology, Washington University-St. Louis, St. Louis, MO 63130, USA; (N.R.F.); (M.D.W.); (R.F.)
- Correspondence: (S.J.S.); (G.P.M.)
| | - Grover P. Miller
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
- Correspondence: (S.J.S.); (G.P.M.)
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23
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Unlocking the Health Potential of Microalgae as Sustainable Sources of Bioactive Compounds. Int J Mol Sci 2021; 22:ijms22094383. [PMID: 33922258 PMCID: PMC8122763 DOI: 10.3390/ijms22094383] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/14/2021] [Accepted: 04/18/2021] [Indexed: 12/15/2022] Open
Abstract
Microalgae are known to produce a plethora of compounds derived from the primary and secondary metabolism. Different studies have shown that these compounds may have allelopathic, antimicrobial, and antipredator activities. In addition, in vitro and in vivo screenings have shown that several compounds have interesting bioactivities (such as antioxidant, anti-inflammatory, anticancer, and antimicrobial) for the possible prevention and treatment of human pathologies. Additionally, the enzymatic pathways responsible for the synthesis of these compounds, and the targets and mechanisms of their action have also been investigated for a few species. However, further research is necessary for their full exploitation and possible pharmaceutical and other industrial applications. Here, we review the current knowledge on the chemical characteristics, biological activities, mechanism of action, and the enzymes involved in the synthesis of microalgal metabolites with potential benefits for human health.
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24
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Hughes TB, Flynn N, Dang NL, Swamidass SJ. Modeling the Bioactivation and Subsequent Reactivity of Drugs. Chem Res Toxicol 2021; 34:584-600. [PMID: 33496184 DOI: 10.1021/acs.chemrestox.0c00417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrophilically reactive drug metabolites are implicated in many adverse drug reactions. In this mechanism-termed bioactivation-metabolic enzymes convert drugs into reactive metabolites that often conjugate to nucleophilic sites within biological macromolecules like proteins. Toxic metabolite-product adducts induce severe immune responses that can cause sometimes fatal disorders, most commonly in the form of liver injury, blood dyscrasia, or the dermatologic conditions toxic epidermal necrolysis and Stevens-Johnson syndrome. This study models four of the most common metabolic transformations that result in bioactivation: quinone formation, epoxidation, thiophene sulfur-oxidation, and nitroaromatic reduction, by synthesizing models of metabolism and reactivity. First, the metabolism models predict the formation probabilities of all possible metabolites among the pathways studied. Second, the exact structures of these metabolites are enumerated. Third, using these structures, the reactivity model predicts the reactivity of each metabolite. Finally, a feedfoward neural network converts the metabolism and reactivity predictions to a bioactivation prediction for each possible metabolite. These bioactivation predictions represent the joint probability that a metabolite forms and that this metabolite subsequently conjugates to protein or glutathione. Among molecules bioactivated by these pathways, we predicted the correct pathway with an AUC accuracy of 89.98%. Furthermore, the model predicts whether molecules will be bioactivated, distinguishing bioactivated and nonbioactivated molecules with 81.06% AUC. We applied this algorithm to withdrawn drugs. The known bioactivation pathways of alclofenac and benzbromarone were identified by the algorithm, and high probability bioactivation pathways not yet confirmed were identified for safrazine, zimelidine, and astemizole. This bioactivation model-the first of its kind that jointly considers both metabolism and reactivity-enables drug candidates to be quickly evaluated for a toxicity risk that often evades detection during preclinical trials. The XenoSite bioactivation model is available at http://swami.wustl.edu/xenosite/p/bioactivation.
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Affiliation(s)
- Tyler B Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Noah Flynn
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Na Le Dang
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - S Joshua Swamidass
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
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25
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Abstract
Myeloperoxidase participates in innate immune defense mechanism through formation of microbicidal reactive oxidants and diffusible radical species. A unique activity is its ability to use chloride as a cosubstrate with hydrogen peroxide to generate chlorinating oxidants such as hypochlorous acid, a potent antimicrobial agent. However, chronic MPO activation can lead to indiscriminate protein modification causing tissue damage, and has been associated with chronic inflammatory diseases, atherosclerosis, and acute cardiovascular events. This has attracted considerable interest in the development of therapeutically useful MPO inhibitors. Today, based on the profound knowledge of structure and function of MPO and its biochemical and biophysical differences with the other homologous human peroxidases, various rational and high-throughput screening attempts were performed in developing specific irreversible and reversible inhibitors. The most prominent candidates as well as MPO inhibitors already studied in clinical trials are introduced and discussed.
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26
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Ushiyama F, Takashima H, Matsuda Y, Ogata Y, Sasamoto N, Kurimoto-Tsuruta R, Ueki K, Tanaka-Yamamoto N, Endo M, Mima M, Fujita K, Takata I, Tsuji S, Yamashita H, Okumura H, Otake K, Sugiyama H. Lead optimization of 2-hydroxymethyl imidazoles as non-hydroxamate LpxC inhibitors: Discovery of TP0586532. Bioorg Med Chem 2020; 30:115964. [PMID: 33385955 DOI: 10.1016/j.bmc.2020.115964] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 11/19/2022]
Abstract
Infectious diseases caused by resistant Gram-negative bacteria have become a serious problem, and the development of therapeutic drugs with a novel mechanism of action and that do not exhibit cross-resistance with existing drugs has been earnestly desired. UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) is a drug target that has been studied for a long time. However, no LpxC inhibitors are available on the market at present. In this study, we sought to create a new antibacterial agent without a hydroxamate moiety, which is a common component of the major LpxC inhibitors that have been reported to date and that may cause toxicity. As a result, a development candidate, TP0586532, was created that is effective against carbapenem-resistant Klebsiella pneumoniae and does not pose a cardiovascular risk.
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Affiliation(s)
- Fumihito Ushiyama
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan.
| | - Hajime Takashima
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Yohei Matsuda
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Yuya Ogata
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Naoki Sasamoto
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | | | - Kaori Ueki
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | | | - Mayumi Endo
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Masashi Mima
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Kiyoko Fujita
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Iichiro Takata
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Satoshi Tsuji
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Haruhiro Yamashita
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Hirotoshi Okumura
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Katsumasa Otake
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Hiroyuki Sugiyama
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
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Aventurado CA, Billones JB, Vasquez RD, Castillo AL. In Ovo and In Silico Evaluation of the Anti-Angiogenic Potential of Syringin. Drug Des Devel Ther 2020; 14:5189-5204. [PMID: 33268982 PMCID: PMC7701684 DOI: 10.2147/dddt.s271952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/08/2020] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Cancer is considered as one of the deadliest human diseases today. Angiogenesis, the propagation of new blood vessels from pre-existing vasculature, is a critical step in the progression of cancer as it is essential in the growth and metastasis of tumors. Hence, suppression of angiogenesis is a promising approach in cancer therapy. Syringin, a phenylpropanoid glycoside with a molecular formula of C17H24O9, has been found to exhibit chemopreventive effects. However, its anti-angiogenic activity and the underlying mechanism of action are still unknown. METHODS In this work, in ovo chorioallantoic membrane (CAM) assay has been conducted to evaluate the effect of syringin on neovascularization. Additionally, reverse molecular docking studies have been performed in order to identify the probable enzyme targets in the angiogenesis pathway. RESULTS Treatment with syringin showed significant dose-dependent inhibition of blood vessel length and junctions in the CAM of duck eggs; the anti-angiogenic activity of syringin at 100 µM and 200 µM is comparable with 200 µM of the positive control celecoxib. The results of reverse docking studies indicate that syringin binds the strongest to dihydrofolate reductase (DHFR) and, to some extent, with transforming growth factor-beta receptor type 1 (TGF-βR1), vascular endothelial growth factor receptor 2 (VEGFR2), and matrix metalloproteinase-2 (MMP-2). Furthermore, ADMET models revealed that syringin potentially possesses excellent pharmacokinetic and toxicity profiles. CONCLUSION This study demonstrates the potential of syringin as an anti-angiogenic agent and elicits further investigations to establish its application in cancer suppression.
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Affiliation(s)
| | - Junie B Billones
- Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila, Philippines
| | - Ross D Vasquez
- The Graduate School, University of Santo Tomas, Manila1015, Philippines
- Faculty of Pharmacy, University of Santo Tomas, Manila1015, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila1015, Philippines
| | - Agnes L Castillo
- The Graduate School, University of Santo Tomas, Manila1015, Philippines
- Faculty of Pharmacy, University of Santo Tomas, Manila1015, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila1015, Philippines
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28
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Liljenberg M, Ripa L, Shamovsky I. Theoretical Studies of the Mechanism of Carbamoylation of Nucleobases by Isocyanates. Chem Res Toxicol 2020; 33:2845-2853. [PMID: 33076655 DOI: 10.1021/acs.chemrestox.0c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isocyanates with the -N═C═O functional group are highly reactive compounds. They are used in various industrial applications and have been found as possible metabolites of hydroxamic acids. Isocyanates interact with biopolymers and are notorious mutagens. Mutagenic effects of isocyanates are caused by the formation of covalent adducts with nucleobases of DNA, primarily cytosines, through carbamoylation of NH2 groups to give the corresponding urea. The mechanism of carbamoylation of nucleobases by aryl isocyanates is studied by high-level density functional theory calculations. Three possible pathways are analyzed. It is demonstrated that the reaction follows the stepwise pathway, which starts with the formation of a π-complex followed by a rate-determining C-N covalent bond formation via the reactive tautomeric imine forms of the nucleobases. The reaction proceeds further through two consecutive proton transfers mediated by water molecules to give the final adduct. The predicted activation free energies of the rate-determining step in water agree with experimental data. In line with experiments, the reactivity of isocyanates toward nucleobases decreases in the order cytosine > adenine > guanine, and we rationalize this order of reactivity by the fall of their basicity and destabilization of the imine forms. Activation barriers of the alternative concerted pathways are higher than that of the preferred stepwise mechanism, and the match to experiment is poor. The kinetic effect of adding electron-withdrawing or electron-donating groups to the aryl group of aryl isocyanate is minute, which suggests that mutagenicity of isocyanates is determined exclusively by the reactivity of the -N═C═O group and as such cannot be removed by structural alterations of the adjacent aryl.
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Affiliation(s)
| | - Lena Ripa
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Igor Shamovsky
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, 431 83 Mölndal, Sweden
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29
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Hughes TB, Dang NL, Kumar A, Flynn NR, Swamidass SJ. Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites. J Chem Inf Model 2020; 60:4702-4716. [PMID: 32881497 PMCID: PMC8716321 DOI: 10.1021/acs.jcim.0c00360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Adverse drug metabolism often severely impacts patient morbidity and mortality. Unfortunately, drug metabolism experimental assays are costly, inefficient, and slow. Instead, computational modeling could rapidly flag potentially toxic molecules across thousands of candidates in the early stages of drug development. Most metabolism models focus on predicting sites of metabolism (SOMs): the specific substrate atoms targeted by metabolic enzymes. However, SOMs are merely a proxy for metabolic structures: knowledge of an SOM does not explicitly provide the actual metabolite structure. Without an explicit metabolite structure, computational systems cannot evaluate the new molecule's properties. For example, the metabolite's reactivity cannot be automatically predicted, a crucial limitation because reactive drug metabolites are a key driver of adverse drug reactions (ADRs). Additionally, further metabolic events cannot be forecast, even though the metabolic path of the majority of substrates includes two or more sequential steps. To overcome the myopia of the SOM paradigm, this study constructs a well-defined system-termed the metabolic forest-for generating exact metabolite structures. We validate the metabolic forest with the substrate and product structures from a large, chemically diverse, literature-derived dataset of 20 736 records. The metabolic forest finds a pathway linking each substrate and product for 79.42% of these records. By performing a breadth-first search of depth two or three, we improve performance to 88.43 and 88.77%, respectively. The metabolic forest includes a specialized algorithm for producing accurate quinone structures, the most common type of reactive metabolite. To our knowledge, this quinone structure algorithm is the first of its kind, as the diverse mechanisms of quinone formation are difficult to systematically reproduce. We validate the metabolic forest on a previously published dataset of 576 quinone reactions, predicting their structures with a depth three performance of 91.84%. The metabolic forest accurately enumerates metabolite structures, enabling promising new directions such as joint metabolism and reactivity modeling.
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Affiliation(s)
- Tyler B Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Na Le Dang
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Ayush Kumar
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Noah R Flynn
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - S Joshua Swamidass
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
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30
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Liu S, Li S, Yuan D, Wang E, Xie R, Zhang W, Kong Y, Zhu X. Protease activated receptor 4 (PAR4) antagonists: Research progress on small molecules in the field of antiplatelet agents. Eur J Med Chem 2020; 209:112893. [PMID: 33049608 DOI: 10.1016/j.ejmech.2020.112893] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 12/27/2022]
Abstract
Protease activated receptor 4 (PAR4) is a key target in antiplatelet medication to reduce the risk of heart attack and thrombotic complications in stroke. PAR4 antagonists can prevent harmful and stable thrombus growth while retaining initial thrombus formation by acting on the late diffusion stage of platelet activation, which may provide a safer alternative than other antiplatelet agents. Currently, research on PAR4 antagonists is of increasing interest in the field of antiplatelet agents. This article provides an overview of the discovery and development of small-molecule antagonists of PAR4 as novel antiplatelet agents, including structure-activity relationship (SAR) analysis, progress of structure and bioassay optimization, and the latest structural and/or clinical information of representative small-molecule antagonists of PAR4.
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Affiliation(s)
- Shangde Liu
- Institute of Medicinal & Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Shanshan Li
- Institute of Medicinal & Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Duo Yuan
- Institute of Medicinal & Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Enmao Wang
- Institute of Medicinal & Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Roujie Xie
- Institute of Medicinal & Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Weiqi Zhang
- Institute of Medicinal & Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yi Kong
- School of Life & Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Xiong Zhu
- Institute of Medicinal & Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China.
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31
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Barnette DA, Schleiff MA, Osborn LR, Flynn N, Matlock M, Swamidass SJ, Miller GP. Dual mechanisms suppress meloxicam bioactivation relative to sudoxicam. Toxicology 2020; 440:152478. [PMID: 32437779 DOI: 10.1016/j.tox.2020.152478] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/17/2020] [Accepted: 04/24/2020] [Indexed: 01/07/2023]
Abstract
Thiazoles are biologically active aromatic heterocyclic rings occurring frequently in natural products and drugs. These molecules undergo typically harmless elimination; however, a hepatotoxic response can occur due to multistep bioactivation of the thiazole to generate a reactive thioamide. A basis for those differences in outcomes remains unknown. A textbook example is the high hepatotoxicity observed for sudoxicam in contrast to the relative safe use and marketability of meloxicam, which differs in structure from sudoxicam by the addition of a single methyl group. Both drugs undergo bioactivation, but meloxicam exhibits an additional detoxification pathway due to hydroxylation of the methyl group. We hypothesized that thiazole bioactivation efficiency is similar between sudoxicam and meloxicam due to the methyl group being a weak electron donator, and thus, the relevance of bioactivation depends on the competing detoxification pathway. For a rapid analysis, we modeled epoxidation of sudoxicam derivatives to investigate the impact of substituents on thiazole bioactivation. As expected, electron donating groups increased the likelihood for epoxidation with a minimal effect for the methyl group, but model predictions did not extrapolate well among all types of substituents. Through analytical methods, we measured steady-state kinetics for metabolic bioactivation of sudoxicam and meloxicam by human liver microsomes. Sudoxicam bioactivation was 6-fold more efficient than that for meloxicam, yet meloxicam showed a 6-fold higher efficiency of detoxification than bioactivation. Overall, sudoxicam bioactivation was 15-fold more likely than meloxicam considering all metabolic clearance pathways. Kinetic differences likely arise from different enzymes catalyzing respective metabolic pathways based on phenotyping studies. Rather than simply providing an alternative detoxification pathway, the meloxicam methyl group suppressed the bioactivation reaction. These findings indicate the impact of thiazole substituents on bioactivation is more complex than previously thought and likely contributes to the unpredictability of their toxic potential.
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Affiliation(s)
- Dustyn A Barnette
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, United States
| | - Mary A Schleiff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, United States
| | - Laura R Osborn
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, United States
| | - Noah Flynn
- Department of Pathology and Immunology, 660 S Euclid Ave, Washington University, St. Louis, MO, 63130, United States
| | - Matthew Matlock
- Department of Pathology and Immunology, 660 S Euclid Ave, Washington University, St. Louis, MO, 63130, United States
| | - S Joshua Swamidass
- Department of Pathology and Immunology, 660 S Euclid Ave, Washington University, St. Louis, MO, 63130, United States
| | - Grover P Miller
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, United States.
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Emerging club drugs: 5-(2-aminopropyl)benzofuran (5-APB) is more toxic than its isomer 6-(2-aminopropyl)benzofuran (6-APB) in hepatocyte cellular models. Arch Toxicol 2019; 94:609-629. [PMID: 31838565 DOI: 10.1007/s00204-019-02638-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/26/2019] [Indexed: 12/15/2022]
Abstract
New phenylethylamine derivatives are among the most commonly abused new psychoactive substances. They are synthesized and marketed in lieu of classical amphetaminic stimulants, with no previous safety testing. Our study aimed to determine the in vitro hepatotoxicity of two benzofurans [6-(2-aminopropyl)benzofuran (6-APB) and 5-(2-aminopropyl)benzofuran (5-APB)] that have been misused as 'legal highs'. Cellular viability was assessed through the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction assay, following 24-h drug exposure of human hepatoma HepaRG cells (EC50 2.62 mM 5-APB; 6.02 mM 6-APB), HepG2 cells (EC50 3.79 mM 5-APB; 8.18 mM 6-APB) and primary rat hepatocytes (EC50 964 μM 5-APB; 1.94 mM 6-APB). Co-incubation of primary hepatocytes, the most sensitive in vitro model, with CYP450 inhibitors revealed a role of metabolism, in particular by CYP3A4, in the toxic effects of both benzofurans. Also, 6-APB and 5-APB concentration-dependently enhanced oxidative stress (significantly increased reactive species and oxidized glutathione, and decreased reduced glutathione levels) and unsettled mitochondrial homeostasis, with disruption of mitochondrial membrane potential and decline of intracellular ATP. Evaluation of cell death mechanisms showed increased caspase-8, -9, and -3 activation, and nuclear morphological changes consistent with apoptosis; at concentrations higher than 2 mM, however, necrosis prevailed. Concentration-dependent formation of acidic vesicular organelles typical of autophagy was also observed for both drugs. Overall, 5-APB displayed higher hepatotoxicity than its 6-isomer. Our findings provide new insights into the potential hepatotoxicity of these so-called 'safe drugs' and highlight the putative risks associated with their use as psychostimulants.
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Filimonov AS, Chepanova AA, Luzina OA, Zakharenko AL, Zakharova OD, Ilina ES, Dyrkheeva NS, Kuprushkin MS, Kolotaev AV, Khachatryan DS, Patel J, Leung IK, Chand R, Ayine-Tora DM, Reynisson J, Volcho KP, Salakhutdinov NF, Lavrik OI. New Hydrazinothiazole Derivatives of Usnic Acid as Potent Tdp1 Inhibitors. Molecules 2019; 24:molecules24203711. [PMID: 31619021 PMCID: PMC6832265 DOI: 10.3390/molecules24203711] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/12/2019] [Accepted: 10/12/2019] [Indexed: 11/16/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a promising therapeutic target in cancer therapy. Combination chemotherapy using Tdp1 inhibitors as a component can potentially improve therapeutic response to many chemotherapeutic regimes. A new set of usnic acid derivatives with hydrazonothiazole pharmacophore moieties were synthesized and evaluated as Tdp1 inhibitors. Most of these compounds were found to be potent inhibitors with IC50 values in the low nanomolar range. The activity of the compounds was verified by binding experiments and supported by molecular modeling. The ability of the most effective inhibitors, used at non-toxic concentrations, to sensitize tumors to the anticancer drug topotecan was also demonstrated. The order of administration of the inhibitor and topotecan on their synergistic effect was studied, suggesting that prior or simultaneous introduction of the inhibitor with topotecan is the most effective.
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Affiliation(s)
- Aleksander S. Filimonov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
- Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
| | - Arina A. Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (A.L.Z.); (O.D.Z.); (E.S.I.); (N.S.D.); (M.S.K.)
| | - Olga A. Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
| | - Alexandra L. Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (A.L.Z.); (O.D.Z.); (E.S.I.); (N.S.D.); (M.S.K.)
| | - Olga D. Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (A.L.Z.); (O.D.Z.); (E.S.I.); (N.S.D.); (M.S.K.)
| | - Ekaterina S. Ilina
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (A.L.Z.); (O.D.Z.); (E.S.I.); (N.S.D.); (M.S.K.)
| | - Nadezhda S. Dyrkheeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (A.L.Z.); (O.D.Z.); (E.S.I.); (N.S.D.); (M.S.K.)
| | - Maxim S. Kuprushkin
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (A.L.Z.); (O.D.Z.); (E.S.I.); (N.S.D.); (M.S.K.)
| | - Anton V. Kolotaev
- The Federal State Unitary Enterprise, Institute of Chemical Reagents and High Purity Chemical Substances of National Research Centre, Kurchatov Institute, 107076 Moscow, Russia; (A.V.K.); (D.S.K.)
| | - Derenik S. Khachatryan
- The Federal State Unitary Enterprise, Institute of Chemical Reagents and High Purity Chemical Substances of National Research Centre, Kurchatov Institute, 107076 Moscow, Russia; (A.V.K.); (D.S.K.)
| | - Jinal Patel
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand; (J.P.); (R.C.); (D.M.A.-T.)
| | - Ivanhoe K.H. Leung
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand; (J.P.); (R.C.); (D.M.A.-T.)
| | - Raina Chand
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand; (J.P.); (R.C.); (D.M.A.-T.)
| | - Daniel M. Ayine-Tora
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand; (J.P.); (R.C.); (D.M.A.-T.)
| | - Johannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Staffordshire ST5 5BG, UK;
| | - Konstantin P. Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
- Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
- Correspondence: (K.P.V.); (O.I.L.); Tel.: +7-383-3308870 (K.P.V.); + 7-383-3635195 (O.I.L.)
| | - Nariman F. Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
- Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
| | - Olga I. Lavrik
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
- Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
- Correspondence: (K.P.V.); (O.I.L.); Tel.: +7-383-3308870 (K.P.V.); + 7-383-3635195 (O.I.L.)
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Da C, Zhang D, Stashko M, Vasileiadi E, Parker R, Minson KA, Huey MG, Huelse JM, Hunter D, Gilbert TSK, Norris-Drouin J, Miley M, Herring LE, Graves LM, DeRyckere D, Earp HS, Graham D, Frye SV, Wang X, Kireev D. Data-Driven Construction of Antitumor Agents with Controlled Polypharmacology. J Am Chem Soc 2019; 141:15700-15709. [PMID: 31497954 PMCID: PMC6894422 DOI: 10.1021/jacs.9b08660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Controlling which particular members of a large protein family are targeted by a drug is key to achieving a desired therapeutic response. In this study, we report a rational data-driven strategy for achieving restricted polypharmacology in the design of antitumor agents selectively targeting the TYRO3, AXL, and MERTK (TAM) family tyrosine kinases. Our computational approach, based on the concept of fragments in structural environments (FRASE), distills relevant chemical information from structural and chemogenomic databases to assemble a three-dimensional inhibitor structure directly in the protein pocket. Target engagement by the inhibitors designed led to disruption of oncogenic phenotypes as demonstrated in enzymatic assays and in a panel of cancer cell lines, including acute lymphoblastic and myeloid leukemia (ALL/AML) and nonsmall cell lung cancer (NSCLC). Structural rationale underlying the approach was corroborated by X-ray crystallography. The lead compound demonstrated potent target inhibition in a pharmacodynamic study in leukemic mice.
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Affiliation(s)
- Chenxiao Da
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Dehui Zhang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Michael Stashko
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Eleana Vasileiadi
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Rebecca Parker
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Katherine A. Minson
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Madeline G. Huey
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Justus M. Huelse
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Debra Hunter
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Thomas S. K. Gilbert
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jacqueline Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Michael Miley
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Laura E. Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lee M. Graves
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Deborah DeRyckere
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - H. Shelton Earp
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Douglas Graham
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xiaodong Wang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
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Antypenko L, Sadykova Z, Shabelnyk K, Meyer F, Kovalenko S, Meyer V, Garbe LA, Steffens K. Synthesis and mode of action studies of novel {2-(3-R-1H-1,2,4-triazol-5-yl)phenyl}amines to combat pathogenic fungi. Arch Pharm (Weinheim) 2019; 352:e1900092. [PMID: 31463959 DOI: 10.1002/ardp.201900092] [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: 03/21/2019] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 11/09/2022]
Abstract
Due to their high specificity and efficacy, triazoles have become versatile antifungals to treat fungal infections in human healthcare and to control phytopathogenic fungi in agriculture. However, azole resistance is an emerging problem affecting human health as well as food security. Here we describe the synthesis of 10 novel {2-(3-R-1H-1,2,4-triazol-5-yl)phenyl}amines. Their structure was ascertained by liquid chromatography-mass spectrometry, 1 H and 13 C NMR, and elemental analysis data. Applying an in vitro growth assay, these triazoles show moderate to significant antifungal activity against the opportunistic pathogen Aspergillus niger, 12 fungi (Fusarium oxysporum, Fusarium fujikuroi, Colletotrichum higginsianum, Gaeumannomyces graminis, Colletotrichum coccodes, Claviceps purpurea, Alternaria alternata, Mucor indicus, Fusarium graminearum, Verticillium lecanii, Botrytis cinerea, Penicillium digitatum) and three oomycetes (Phytophtora infestans GL-1, P. infestans 4/91; R+ and 4/91; R-) in the concentration range from 1 to 50 µg/ml (0.003-2.1 μM). Frontier molecular orbital energies were determined to predict their genotoxic potential. Molecular docking calculations taking into account six common fungal enzymes point to 14α-demethylase (CYP51) and N-myristoyltransferase as the most probable fungal targets. With respect to effectiveness, structure-activity calculations revealed the strong enhancing impact of adamantyl residues. The shown nonmutagenicity in the Salmonella reverse-mutagenicity assay and no violations of drug-likeness parameters suggest the good bioavailability and attractive ecotoxicological profile of the studied triazoles.
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Affiliation(s)
- Lyudmyla Antypenko
- Department of Food and Bioproduct Technology, Neubrandenburg University, Neubrandenburg, Germany
| | - Zhanar Sadykova
- Department of Food and Bioproduct Technology, Neubrandenburg University, Neubrandenburg, Germany
| | - Kostiantyn Shabelnyk
- Departments of Pharmaceutical Chemistry, Organic and Bioorganic Chemistry, Zaporizhzhya State Medical University, Zaporizhzhya, Ukraine
| | - Fatuma Meyer
- Department of Food and Bioproduct Technology, Neubrandenburg University, Neubrandenburg, Germany
| | - Sergiy Kovalenko
- Departments of Pharmaceutical Chemistry, Organic and Bioorganic Chemistry, Zaporizhzhya State Medical University, Zaporizhzhya, Ukraine
| | - Vera Meyer
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Leif-Alexander Garbe
- Department of Food and Bioproduct Technology, Neubrandenburg University, Neubrandenburg, Germany
| | - Karl Steffens
- Department of Food and Bioproduct Technology, Neubrandenburg University, Neubrandenburg, Germany
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Cohen F, Aggen JB, Andrews LD, Assar Z, Boggs J, Choi T, Dozzo P, Easterday AN, Haglund CM, Hildebrandt DJ, Holt MC, Joly K, Jubb A, Kamal Z, Kane TR, Konradi AW, Krause KM, Linsell MS, Machajewski TD, Miroshnikova O, Moser HE, Nieto V, Phan T, Plato C, Serio AW, Seroogy J, Shakhmin A, Stein AJ, Sun AD, Sviridov S, Wang Z, Wlasichuk K, Yang W, Zhou X, Zhu H, Cirz RT. Optimization of LpxC Inhibitors for Antibacterial Activity and Cardiovascular Safety. ChemMedChem 2019; 14:1560-1572. [DOI: 10.1002/cmdc.201900287] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/03/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Frederick Cohen
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - James B. Aggen
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Logan D. Andrews
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Zahra Assar
- Cayman Chemical Co. 1180 East Ellsworth Ann Arbor MI 48108 USA
| | - Jen Boggs
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Taylor Choi
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Paola Dozzo
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | | | - Cat M. Haglund
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | | | - Melissa C. Holt
- Cayman Chemical Co. 1180 East Ellsworth Ann Arbor MI 48108 USA
| | - Kristin Joly
- Plato BioPharma Inc. 7581 West 103rd Avenue, Unit 300 Westminster CO 80021 USA
| | - Adrian Jubb
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Zeeshan Kamal
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | - Timothy R. Kane
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | | | - Kevin M. Krause
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Martin S. Linsell
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | | | | | - Heinz E. Moser
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Vincent Nieto
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Thu Phan
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | - Craig Plato
- Plato BioPharma Inc. 7581 West 103rd Avenue, Unit 300 Westminster CO 80021 USA
| | - Alisa W. Serio
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Julie Seroogy
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Anton Shakhmin
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | - Adam J. Stein
- Cayman Chemical Co. 1180 East Ellsworth Ann Arbor MI 48108 USA
| | - Alex D. Sun
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | | | - Zhan Wang
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | - Kenneth Wlasichuk
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
| | - Wen Yang
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | - Xiaoming Zhou
- Pharmaron Inc. 6 Tai-He Road, BDA Beijing 100176 China
| | - Hai Zhu
- Nanosyn Inc. 3100 Central Expressway Santa Clara CA 95051 USA
| | - Ryan T. Cirz
- Achaogen Inc. 1 Tower Place, Suite 400 South San Francisco CA 94080 USA
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37
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Norcross NR, Wilson C, Baragaña B, Hallyburton I, Osuna‐Cabello M, Norval S, Riley J, Fletcher D, Sinden R, Delves M, Ruecker A, Duffy S, Meister S, Antonova‐Koch Y, Crespo B, de Cózar C, Sanz LM, Gamo FJ, Avery VM, Frearson JA, Gray DW, Fairlamb AH, Winzeler EA, Waterson D, Campbell SF, Willis PA, Read KD, Gilbert IH. Substituted Aminoacetamides as Novel Leads for Malaria Treatment. ChemMedChem 2019; 14:1329-1335. [PMID: 31188540 PMCID: PMC6899483 DOI: 10.1002/cmdc.201900329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Indexed: 01/29/2023]
Abstract
Herein we describe the optimization of a phenotypic hit against Plasmodium falciparum based on an aminoacetamide scaffold. This led to N-(3-chloro-4-fluorophenyl)-2-methyl-2-{[4-methyl-3-(morpholinosulfonyl)phenyl]amino}propanamide (compound 28) with low-nanomolar activity against the intraerythrocytic stages of the malaria parasite, and which was found to be inactive in a mammalian cell counter-screen up to 25 μm. Inhibition of gametes in the dual gamete activation assay suggests that this family of compounds may also have transmission blocking capabilities. Whilst we were unable to optimize the aqueous solubility and microsomal stability to a point at which the aminoacetamides would be suitable for in vivo pharmacokinetic and efficacy studies, compound 28 displayed excellent antimalarial potency and selectivity; it could therefore serve as a suitable chemical tool for drug target identification.
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Affiliation(s)
- Neil R. Norcross
- Drug Discovery UnitDivision of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDundeeDD1 5EHUK
| | - Caroline Wilson
- Drug Discovery UnitDivision of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDundeeDD1 5EHUK
| | - Beatriz Baragaña
- Drug Discovery UnitDivision of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDundeeDD1 5EHUK
| | - Irene Hallyburton
- Drug Discovery UnitDivision of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDundeeDD1 5EHUK
| | - Maria Osuna‐Cabello
- Drug Discovery UnitDivision of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDundeeDD1 5EHUK
| | - Suzanne Norval
- Drug Discovery UnitDivision of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDundeeDD1 5EHUK
| | - Jennifer Riley
- Drug Discovery UnitDivision of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDundeeDD1 5EHUK
| | - Daniel Fletcher
- Drug Discovery UnitDivision of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDundeeDD1 5EHUK
| | | | | | | | - Sandra Duffy
- Discovery BiologyGriffith Institute for Drug DiscoveryGriffith UniversityNathanQueensland4111Australia
| | - Stephan Meister
- Department of PediatricsUniversity of California San Diego School of Medicine9500 Gilman Drive 0741La JollaCA92093USA
| | - Yevgeniya Antonova‐Koch
- Department of PediatricsUniversity of California San Diego School of Medicine9500 Gilman Drive 0741La JollaCA92093USA
| | - Benigno Crespo
- GlaxoSmithKline, Diseases of the Developing World – Tres Cantos Medicines Development Campusc/ Severo Ochoa 2, Tres Cantos28760MadridSpain
| | - Cristina de Cózar
- GlaxoSmithKline, Diseases of the Developing World – Tres Cantos Medicines Development Campusc/ Severo Ochoa 2, Tres Cantos28760MadridSpain
| | - Laura M. Sanz
- GlaxoSmithKline, Diseases of the Developing World – Tres Cantos Medicines Development Campusc/ Severo Ochoa 2, Tres Cantos28760MadridSpain
| | - Francisco Javier Gamo
- GlaxoSmithKline, Diseases of the Developing World – Tres Cantos Medicines Development Campusc/ Severo Ochoa 2, Tres Cantos28760MadridSpain
| | - Vicky M. Avery
- Discovery BiologyGriffith Institute for Drug DiscoveryGriffith UniversityNathanQueensland4111Australia
| | - Julie A. Frearson
- Drug Discovery UnitDivision of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDundeeDD1 5EHUK
| | - David W. Gray
- Drug Discovery UnitDivision of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDundeeDD1 5EHUK
| | - Alan H. Fairlamb
- Drug Discovery UnitDivision of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDundeeDD1 5EHUK
| | - Elizabeth A. Winzeler
- Department of PediatricsUniversity of California San Diego School of Medicine9500 Gilman Drive 0741La JollaCA92093USA
| | - David Waterson
- Medicines for Malaria VentureInternational Centre, Cointrin, Entrance G, 3rd FloorRoute de Pré-Bois 20, PO Box 1826Geneva1215Switzerland
| | - Simon F. Campbell
- Medicines for Malaria VentureInternational Centre, Cointrin, Entrance G, 3rd FloorRoute de Pré-Bois 20, PO Box 1826Geneva1215Switzerland
| | - Paul A. Willis
- Medicines for Malaria VentureInternational Centre, Cointrin, Entrance G, 3rd FloorRoute de Pré-Bois 20, PO Box 1826Geneva1215Switzerland
| | - Kevin D. Read
- Drug Discovery UnitDivision of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDundeeDD1 5EHUK
| | - Ian H. Gilbert
- Drug Discovery UnitDivision of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDundeeDD1 5EHUK
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38
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Neumann U, Ufer M, Jacobson LH, Rouzade-Dominguez ML, Huledal G, Kolly C, Lüönd RM, Machauer R, Veenstra SJ, Hurth K, Rueeger H, Tintelnot-Blomley M, Staufenbiel M, Shimshek DR, Perrot L, Frieauff W, Dubost V, Schiller H, Vogg B, Beltz K, Avrameas A, Kretz S, Pezous N, Rondeau JM, Beckmann N, Hartmann A, Vormfelde S, David OJ, Galli B, Ramos R, Graf A, Lopez Lopez C. The BACE-1 inhibitor CNP520 for prevention trials in Alzheimer's disease. EMBO Mol Med 2019; 10:emmm.201809316. [PMID: 30224383 PMCID: PMC6220303 DOI: 10.15252/emmm.201809316] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The beta‐site amyloid precursor protein cleaving enzyme‐1 (BACE‐1) initiates the generation of amyloid‐β (Aβ), and the amyloid cascade leading to amyloid plaque deposition, neurodegeneration, and dementia in Alzheimer's disease (AD). Clinical failures of anti‐Aβ therapies in dementia stages suggest that treatment has to start in the early, asymptomatic disease states. The BACE‐1 inhibitor CNP520 has a selectivity, pharmacodynamics, and distribution profile suitable for AD prevention studies. CNP520 reduced brain and cerebrospinal fluid (CSF) Aβ in rats and dogs, and Aβ plaque deposition in APP‐transgenic mice. Animal toxicology studies of CNP520 demonstrated sufficient safety margins, with no signs of hair depigmentation, retina degeneration, liver toxicity, or cardiovascular effects. In healthy adults ≥ 60 years old, treatment with CNP520 was safe and well tolerated and resulted in robust and dose‐dependent Aβ reduction in the cerebrospinal fluid. Thus, long‐term, pivotal studies with CNP520 have been initiated in the Generation Program.
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Affiliation(s)
- Ulf Neumann
- Neuroscience, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Mike Ufer
- Translational Medicine, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Laura H Jacobson
- Neuroscience, Novartis Institute for BioMedical Research, Basel, Switzerland
| | | | - Gunilla Huledal
- PK Sciences, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Carine Kolly
- Preclinical Safety, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Rainer M Lüönd
- Global Discovery Chemistry, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Rainer Machauer
- Global Discovery Chemistry, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Siem J Veenstra
- Global Discovery Chemistry, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Konstanze Hurth
- Global Discovery Chemistry, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Heinrich Rueeger
- Global Discovery Chemistry, Novartis Institute for BioMedical Research, Basel, Switzerland
| | | | | | - Derya R Shimshek
- Neuroscience, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Ludovic Perrot
- Neuroscience, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Wilfried Frieauff
- Preclinical Safety, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Valerie Dubost
- Preclinical Safety, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Hilmar Schiller
- PK Sciences, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Barbara Vogg
- PK Sciences, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Karen Beltz
- PK Sciences, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Alexandre Avrameas
- Biomarker Discovery, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Sandrine Kretz
- Biomarker Discovery, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Nicole Pezous
- Translational Medicine, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Jean-Michel Rondeau
- Chemical Biology and Therapeutics, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Nicolau Beckmann
- Musculoskeletal Diseases, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Andreas Hartmann
- Preclinical Safety, Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Stefan Vormfelde
- Translational Medicine, Novartis Institute for BioMedical Research, Basel, Switzerland
| | | | - Bruno Galli
- Global Drug Development, Novartis, Basel, Switzerland
| | - Rita Ramos
- Global Drug Development, Novartis, Basel, Switzerland
| | - Ana Graf
- Global Drug Development, Novartis, Basel, Switzerland
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39
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Zakharenko A, Dyrkheeva N, Lavrik O. Dual DNA topoisomerase 1 and tyrosyl-DNA phosphodiesterase 1 inhibition for improved anticancer activity. Med Res Rev 2019; 39:1427-1441. [PMID: 31004352 DOI: 10.1002/med.21587] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 03/26/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a DNA repair enzyme that catalyzes the hydrolysis of the phosphodiester bond in the DNA-topoisomerase 1 (Top1) covalent complex and repairs some other 3'-end DNA adducts. Currently, Tdp1 functions as an important target in cancer drug design owing to its ability to break down various DNA adducts induced by chemotherapeutics. Tdp1 inhibitors may sensitize tumor cells to the action of Top1 poisons, thereby potentiating their effects. This mini-review summarizes findings from studies reporting the combined inhibition of Top1 and Tdp1. Two different approaches have been considered for developing such drug precursors.
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Affiliation(s)
- Alexandra Zakharenko
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Nadezhda Dyrkheeva
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Olga Lavrik
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation
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40
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5-Arylidene(chromenyl-methylene)-thiazolidinediones: Potential New Agents against Mutant Oncoproteins K-Ras, N-Ras and B-Raf in Colorectal Cancer and Melanoma. ACTA ACUST UNITED AC 2019; 55:medicina55040085. [PMID: 30935124 PMCID: PMC6524019 DOI: 10.3390/medicina55040085] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/05/2019] [Accepted: 03/28/2019] [Indexed: 01/16/2023]
Abstract
Background and objectives: Cancer represents the miscommunication between and within the body cells. The mutations of the oncogenes encoding the MAPK pathways play an important role in the development of tumoral diseases. The mutations of KRAS and BRAF oncogenes are involved in colorectal cancer and melanoma, while the NRAS mutations are associated with melanoma. Thiazolidine-2,4-dione is a versatile scaffold in medicinal chemistry and a useful tool in the development of new antitumoral compounds. The aim of our study was to predict the pharmacokinetic/pharmacodynamic properties, the drug-likeness and lead-likeness of two series of synthetic 5-arylidene(chromenyl-methylene)-thiazolidinediones, the molecular docking on the oncoproteins K-Ras, N-Ras and B-Raf, and to investigate the cytotoxicity of the compounds, in order to select the best structural profile for potential anticancer agents. Materials and Methods: In our paper we studied the cytotoxicity of two series of thiazolidine-2,4-dione derivatives, their ADME-Tox properties and the molecular docking on a mutant protein of K-Ras, two isoforms of N-Ras and an isoform of B-Raf with 16 mutations. Results: The heterocyclic compounds strongly interact with K-Ras and N-Ras right after their posttranslational processing and/or compete with GDP for the nucleotide-binding site of the two GTPases. They are less active against the GDP-bound states of the two targets. All derivatives have a similar binding pattern in the active site of B-Raf. Conclusions: The data obtained encourage the further investigation of the 5-arylidene(chromenyl-methylene)-thiazolidinediones as potential new agents against the oncoproteins K-Ras, N-Ras and B-Raf.
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41
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Novel acyl thiourea derivatives: Synthesis, antifungal activity, gene toxicity, drug-like and molecular docking screening. Arch Pharm (Weinheim) 2018; 352:e1800275. [DOI: 10.1002/ardp.201800275] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/03/2018] [Accepted: 11/11/2018] [Indexed: 12/18/2022]
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42
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L'abbate FP, Müller R, Openshaw R, Combrinck JM, de Villiers KA, Hunter R, Egan TJ. Hemozoin inhibiting 2-phenylbenzimidazoles active against malaria parasites. Eur J Med Chem 2018; 159:243-254. [PMID: 30296683 DOI: 10.1016/j.ejmech.2018.09.060] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/22/2018] [Accepted: 09/24/2018] [Indexed: 12/23/2022]
Abstract
The 2-phenylbenzimidazole scaffold has recently been discovered to inhibit β-hematin (synthetic hemozoin) formation by high throughput screening. Here, a library of 325,728 N-4-(1H-benzo[d]imidazol-2-yl)aryl)benzamides was enumerated, and Bayesian statistics used to predict β-hematin and Plasmodium falciparum growth inhibition. Filtering predicted inactives and compounds with negligible aqueous solubility reduced the library to 35,124. Further narrowing to compounds with terminal aryl ring substituents only, reduced the library to 18, 83% of which were found to inhibit β-hematin formation <100 μM and 50% parasite growth <2 μM. Four compounds showed nanomolar parasite growth inhibition activities, no cross-resistance in a chloroquine resistant strain and low cytotoxicity. QSAR analysis showed a strong association of parasite growth inhibition with inhibition of β-hematin formation and the most active compound inhibited hemozoin formation in P. falciparum, with consequent increasing exchangeable heme. Pioneering use of molecular docking for this system demonstrated predictive ability and could rationalize observed structure activity trends.
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Affiliation(s)
- Fabrizio P L'abbate
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Ronel Müller
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Roxanne Openshaw
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Jill M Combrinck
- Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, Observatory, 7925, South Africa
| | - Katherine A de Villiers
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Roger Hunter
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Timothy J Egan
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701, South Africa.
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43
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Abbott JR, Patel PA, Howes JE, Akan DT, Kennedy JP, Burns MC, Browning CF, Sun Q, Rossanese OW, Phan J, Waterson AG, Fesik SW. Discovery of Quinazolines That Activate SOS1-Mediated Nucleotide Exchange on RAS. ACS Med Chem Lett 2018; 9:941-946. [PMID: 30258545 DOI: 10.1021/acsmedchemlett.8b00296] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/08/2018] [Indexed: 12/13/2022] Open
Abstract
Proteins in the RAS family are important regulators of cellular signaling and, when mutated, can drive cancer pathogenesis. Despite considerable effort over the last 30 years, RAS proteins have proven to be recalcitrant therapeutic targets. One approach for modulating RAS signaling is to target proteins that interact with RAS, such as the guanine nucleotide exchange factor (GEF) son of sevenless homologue 1 (SOS1). Here, we report hit-to-lead studies on quinazoline-containing compounds that bind to SOS1 and activate nucleotide exchange on RAS. Using structure-based design, we refined the substituents attached to the quinazoline nucleus and built in additional interactions not present in the initial HTS hit. Optimized compounds activate nucleotide exchange at single-digit micromolar concentrations in vitro. In HeLa cells, these quinazolines increase the levels of RAS-GTP and cause signaling changes in the mitogen-activated protein kinase/extracellular regulated kinase (MAPK/ERK) pathway.
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Affiliation(s)
- Jason R. Abbott
- Department of Biochemistry and ‡Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Pratiq A. Patel
- Department of Biochemistry and ‡Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Jennifer E. Howes
- Department of Biochemistry and ‡Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Denis T. Akan
- Department of Biochemistry and ‡Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - J. Phillip Kennedy
- Department of Biochemistry and ‡Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Michael C. Burns
- Department of Biochemistry and ‡Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Carrie F. Browning
- Department of Biochemistry and ‡Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Qi Sun
- Department of Biochemistry and ‡Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Olivia W. Rossanese
- Department of Biochemistry and ‡Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Jason Phan
- Department of Biochemistry and ‡Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Alex G. Waterson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-0146, United States
| | - Stephen W. Fesik
- Department of Biochemistry and ‡Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-0146, United States
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44
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Zhang Z, Tang W. Drug metabolism in drug discovery and development. Acta Pharm Sin B 2018; 8:721-732. [PMID: 30245961 PMCID: PMC6146880 DOI: 10.1016/j.apsb.2018.04.003] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/25/2018] [Accepted: 04/02/2018] [Indexed: 11/27/2022] Open
Abstract
Drug metabolism as a discipline plays an important role in drug discovery and development and the effects of drug metabolism on pharmacokinetics (PK), pharmacodynamics (PD), and safety should be carefully considered. This communication provides an overview of common strategies in the area of drug metabolism for improving PK/PD and safety profiles of drug candidates; these include, but are not limited to, collaboration with medicinal chemists on structure–activity relationships (SAR) to overcome high clearance, using deuterium replacement to further optimize a lead, prodrug approaches to circumvent formulation and delivery difficulties, and addressing issues such as species differences in metabolism, drug–drug interactions (DDI) and formation of reactive metabolites.
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45
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Hevener KE. Computational Toxicology Methods in Chemical Library Design and High-Throughput Screening Hit Validation. Methods Mol Biol 2018; 1800:275-285. [PMID: 29934898 DOI: 10.1007/978-1-4939-7899-1_13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The discovery of molecular toxicity in a clinical drug candidate can have a significant impact on both the cost and timeline of the drug discovery process. Early identification of potentially toxic compounds during screening library preparation or, alternatively, during the hit validation process, is critical to ensure that valuable time and resources are not spent pursuing compounds that may possess a high propensity for human toxicity. This chapter focuses on the application of computational molecular filters, applied either prescreening or postscreening, to identify and remove known reactive and/or potentially toxic compounds from consideration in drug discovery campaigns.
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Affiliation(s)
- Kirk E Hevener
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA.
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46
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Song F, Cui L, Piao J, Liang H, Si H, Duan Y, Zhai H. Quantitative structure-activity relationship and molecular docking studies on designing inhibitors of the perforin. Chem Biol Drug Des 2017; 90:535-544. [PMID: 28296049 DOI: 10.1111/cbdd.12975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 01/03/2017] [Accepted: 02/24/2017] [Indexed: 01/24/2023]
Abstract
Quantitative structure-activity relationship (QSAR) studies were performed on a series of 5-arylidene-2thioxoimidazolidin-4-ones derivatives as the inhibitors of perforin and to gain insights about the structural determinants for designing new drug molecules. The heuristic method could explore the descriptors responsible for bioactivity and gain a best linear model with R2 .82. Gene expression programming method generated a novel nonlinear function model with R2 .92 for training set and R2 .85 for test set. The predicted IC50 by QSAR, molecular docking analysis, and property explorer applet show that 42a acts as a well-pleasing potent inhibitor for perforin. This study may lay a reliable theoretical foundation for the development of designing perforin inhibitor structures.
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Affiliation(s)
- Fucheng Song
- Department of Public Health, Qingdao University Medical College, Qingdao, Shandong, China
| | - Lianhua Cui
- Department of Public Health, Qingdao University Medical College, Qingdao, Shandong, China
| | - Jinmei Piao
- Department of Public Health, Qingdao University Medical College, Qingdao, Shandong, China
| | - Hui Liang
- Department of Public Health, Qingdao University Medical College, Qingdao, Shandong, China
| | - Hongzong Si
- Institute for Computational Science and Engineering, Laboratory of New Fibrous Materials and Modern Textile, The Growing Base for State Key Laboratory, Qingdao University, Qingdao, Shandong, China
| | - Yunbo Duan
- Institute for Computational Science and Engineering, Laboratory of New Fibrous Materials and Modern Textile, The Growing Base for State Key Laboratory, Qingdao University, Qingdao, Shandong, China
| | - Honglin Zhai
- Department of Chemistry, Lanzhou University, Lanzhou, Gansu, China
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47
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Hirose W, Kato Y, Natsutani I, Takata M, Kitaichi M, Imai S, Hayashi S, Arai Y, Hoshino K, Yoshida K. Synthesis and optimization of 4,5,6,7-tetrahydrooxazolo[4,5-c]pyridines as potent and orally-active metabotropic glutamate receptor 5 negative allosteric modulators. Bioorg Med Chem Lett 2017; 27:4331-4335. [PMID: 28838696 DOI: 10.1016/j.bmcl.2017.08.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 11/28/2022]
Abstract
We describe here the design, synthesis and characterization of a series of 4,5,6,7-tetrahydrooxazolo[4,5-c]pyridines as metabotropic glutamate receptor (mGluR) 5 negative allosteric modulators (NAMs). Optimization of the substituents led to the identification of several compounds with good pharmacokinetic profiles, including long half life and high oral bioavailability, in both rats and monkeys. The receptor occupancy test in the rat cortex revealed favorable brain penetration of these compounds. The reprsentative compound 13 produced oral antidepressant-like effect in the rat forced swimming test (MED: 0.3mg/kg, q.d.).
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Affiliation(s)
- Wataru Hirose
- Drug Research Division, Sumitomo Dainippon Pharma, 3-1-98 Kasugade-naka, Konohana-ku, Osaka 554-0022, Japan.
| | - Yoshihiro Kato
- Drug Research Division, Sumitomo Dainippon Pharma, 3-1-98 Kasugade-naka, Konohana-ku, Osaka 554-0022, Japan
| | - Itaru Natsutani
- Drug Research Division, Sumitomo Dainippon Pharma, 33-94 Enoki-cho, Suita, Osaka 564-0053, Japan
| | - Makoto Takata
- Drug Research Division, Sumitomo Dainippon Pharma, 3-1-98 Kasugade-naka, Konohana-ku, Osaka 554-0022, Japan
| | - Maiko Kitaichi
- Drug Research Division, Sumitomo Dainippon Pharma, 3-1-98 Kasugade-naka, Konohana-ku, Osaka 554-0022, Japan
| | - Satoki Imai
- Drug Research Division, Sumitomo Dainippon Pharma, 33-94 Enoki-cho, Suita, Osaka 564-0053, Japan
| | - Shun Hayashi
- Drug Research Division, Sumitomo Dainippon Pharma, 33-94 Enoki-cho, Suita, Osaka 564-0053, Japan
| | - Yukiyo Arai
- Drug Research Division, Sumitomo Dainippon Pharma, 3-1-98 Kasugade-naka, Konohana-ku, Osaka 554-0022, Japan
| | - Kohei Hoshino
- Drug Research Division, Sumitomo Dainippon Pharma, 3-1-98 Kasugade-naka, Konohana-ku, Osaka 554-0022, Japan
| | - Kohzo Yoshida
- Drug Research Division, Sumitomo Dainippon Pharma, 3-1-98 Kasugade-naka, Konohana-ku, Osaka 554-0022, Japan.
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48
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Pensa AV, Cinelli MA, Li H, Chreifi G, Mukherjee P, Roman LJ, Martásek P, Poulos TL, Silverman RB. Hydrophilic, Potent, and Selective 7-Substituted 2-Aminoquinolines as Improved Human Neuronal Nitric Oxide Synthase Inhibitors. J Med Chem 2017; 60:7146-7165. [PMID: 28776992 DOI: 10.1021/acs.jmedchem.7b00835] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neuronal nitric oxide synthase (nNOS) is a target for development of antineurodegenerative agents. Most nNOS inhibitors mimic l-arginine and have poor bioavailability. 2-Aminoquinolines showed promise as bioavailable nNOS inhibitors but suffered from low human nNOS inhibition, low selectivity versus human eNOS, and significant binding to other CNS targets. We aimed to improve human nNOS potency and selectivity and reduce off-target binding by (a) truncating the original scaffold or (b) introducing a hydrophilic group to interrupt the lipophilic, promiscuous pharmacophore and promote interaction with human nNOS-specific His342. We synthesized both truncated and polar 2-aminoquinoline derivatives and assayed them against recombinant NOS enzymes. Although aniline and pyridine derivatives interact with His342, benzonitriles conferred the best rat and human nNOS inhibition. Both introduction of a hydrophobic substituent next to the cyano group and aminoquinoline methylation considerably improved isoform selectivity. Most importantly, these modifications preserved Caco-2 permeability and reduced off-target CNS binding.
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Affiliation(s)
- Anthony V Pensa
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University , Evanston, Illinois 60208-3113, United States
| | - Maris A Cinelli
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University , Evanston, Illinois 60208-3113, United States
| | - Huiying Li
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
| | - Georges Chreifi
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
| | - Paramita Mukherjee
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University , Evanston, Illinois 60208-3113, United States
| | - Linda J Roman
- Department of Biochemistry, University of Texas Health Science Center , San Antonio, Texas 78384-7760, United States
| | - Pavel Martásek
- Department of Biochemistry, University of Texas Health Science Center , San Antonio, Texas 78384-7760, United States.,Department of Pediatrics and Center for Applied Genomics, First School of Medicine, Charles University and BIOCEV 121 08 Prague, Czech Republic
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
| | - Richard B Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University , Evanston, Illinois 60208-3113, United States
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49
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Majellaro M, Stefanachi A, Tardia P, Vicenti C, Boccarelli A, Pannunzio A, Campanella F, Coluccia M, Denora N, Leonetti F, de Candia M, Altomare CD, Cellamare S. Investigating Structural Requirements for the Antiproliferative Activity of Biphenyl Nicotinamides. ChemMedChem 2017; 12:1380-1389. [PMID: 28665505 DOI: 10.1002/cmdc.201700365] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 11/09/2022]
Abstract
A number of trimethoxybenzoic acid anilides, previously studied as permeability glycoprotein (P-gp) modulators, were screened with the aim of identifying new anticancer agents. One of these compounds, which showed antiproliferative activity against resistant MCF-7 cell line, was selected as the hit structure. Replacement of the trimethoxybenzoyl moiety with a nicotinoyl group, in order to overcome solubility issues, led to a new series of N-biphenyl nicotinoyl anilides, among which a nitro derivative, N-(3',5'-difluoro-3-nitro-[1,1'-biphenyl]-4-yl)nicotinamide (3), displayed antiproliferative activity against MCF-7 and MDA-MB-231 cells in the nanomolar range. The search for a bioisostere of the nitro group led to nitrile analogue N-(3-cyano-4'-fluoro-[1,1'-biphenyl]-4-yl)nicotinamide (36), which shows a strong increase in activity against MCF-7 and MDA-MB-231 cells. Compound 36 induced a dose-dependent accumulation of G2 - and M-phase MCF-7 cell populations, and a decrease in S-phase cells. Relative to vinblastine, a well-known potent antimitotic agent, compound 36 also induced G1 -phase arrest at low doses (20-40 nm), but did not inhibit in vitro tubulin polymerization.
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Affiliation(s)
- Maria Majellaro
- Department of Pharmacy-Drug Sciences, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | - Angela Stefanachi
- Department of Pharmacy-Drug Sciences, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | - Piero Tardia
- D3-Drug Discovery and Development Department, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Chiara Vicenti
- Department of Emergency and Organ Transplantation, Section of Pathological Anatomy, University of Bari, Piazza Giulio Cesare 11, 70124, Bari, Italy
| | - Angelina Boccarelli
- Department of Biomedical Sciences and Human Oncology, University of Bari, Piazza Giulio Cesare 11, 70124, Bari, Italy
| | - Alessandra Pannunzio
- Department of Pharmacy-Drug Sciences, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | - Federica Campanella
- Department of Pharmacy-Drug Sciences, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | - Mauro Coluccia
- Department of Pharmacy-Drug Sciences, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | - Nunzio Denora
- Department of Pharmacy-Drug Sciences, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | - Francesco Leonetti
- Department of Pharmacy-Drug Sciences, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | - Modesto de Candia
- Department of Pharmacy-Drug Sciences, University of Bari, Via Orabona 4, 70125, Bari, Italy
| | | | - Saverio Cellamare
- Department of Pharmacy-Drug Sciences, University of Bari, Via Orabona 4, 70125, Bari, Italy
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50
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Hillard CJ, Huang H, Vogt CD, Rodrigues BE, Neumann TS, Sem DS, Schroeder F, Cunningham CW. Endocannabinoid Transport Proteins: Discovery of Tools to Study Sterol Carrier Protein-2. Methods Enzymol 2017; 593:99-121. [PMID: 28750817 PMCID: PMC6904209 DOI: 10.1016/bs.mie.2017.06.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The endocannabinoid (eCB) neurotransmitter system regulates diverse neurological functions including stress and anxiety, pain, mood, and reward. Understanding the mechanisms underlying eCB regulation is critical for developing targeted pharmacotherapies to treat these and other neurologic disorders. Cellular studies suggest that the arachidonate eCBs, N-arachidonoylethanolamine (AEA) and 2-arachidonoylglycerol (2-AG), are substrates for intracellular binding and transport proteins, and several candidate proteins have been identified. Initial evidence from our laboratory indicates that the lipid transport protein, sterol carrier protein 2 (SCP-2), binds to the eCBs and can regulate their cellular concentrations. Here, we present methods for evaluating SCP-2 binding of eCBs and their application to the discovery of the first inhibitor lead molecules. Using a fluorescent probe displacement assay, we found SCP-2 binds the eCBs, AEA (Ki=0.68±0.05μM) and 2-AG (Ki=0.37±0.02μM), with moderate affinity. A series of structurally diverse arachidonate analogues also bind SCP-2 with Ki values between 0.82 and 2.95μM, suggesting a high degree of tolerance for arachidonic acid head group modifications in this region of the protein. We also report initial structure-activity relationships surrounding previously reported inhibitors of Aedis aegypti SCP-2, and the results of an in silico high-throughput screen that identified structurally novel SCP-2 inhibitor leads. The methods and results reported here provide the basis for a robust probe discovery effort to fully elucidate the role of facilitated transport mediated by SCP-2 in eCB regulation and function.
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Affiliation(s)
| | - Huan Huang
- Texas A&M University, TVMC, College Station, TX, United States
| | - Caleb D Vogt
- Concordia University Wisconsin School of Pharmacy, Mequon, WI, United States
| | - Beatriz E Rodrigues
- Concordia University Wisconsin School of Pharmacy, Mequon, WI, United States
| | - Terrence S Neumann
- Concordia University Wisconsin School of Pharmacy, Mequon, WI, United States; Texas Wesleyan University, Fort Worth, TX, United States
| | - Daniel S Sem
- Concordia University Wisconsin School of Pharmacy, Mequon, WI, United States
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