1
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Tan BH, Ahemad N, Pan Y, Ong CE. Mechanism-based inactivation of cytochromes P450: implications in drug interactions and pharmacotherapy. Xenobiotica 2024:1-24. [PMID: 39175333 DOI: 10.1080/00498254.2024.2395557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 08/17/2024] [Accepted: 08/19/2024] [Indexed: 08/24/2024]
Abstract
Cytochrome P40 (CYP) enzymes dominate the metabolism of numerous endogenous and xenobiotic substances. While it is commonly believed that CYP-catalysed reactions result in the detoxication of foreign substances, these reactions can also yield reactive intermediates that can bind to cellular macromolecules to cause cytotoxicity or irreversibly inactivate CYPs that create them.Mechanism-based inactivation (MBI) produces either irreversible or quasi-irreversible inactivation and is commonly caused by CYP metabolic bioactivation to an electrophilic reactive intermediate. Many drugs that have been known to cause MBI in CYPs have been discovered as perpetrators in drug-drug interactions throughout the last 20-30 years.This review will highlight the key findings from the recent literature about the mechanisms of CYP enzyme inhibition, with a focus on the broad mechanistic elements of MBI for widely used drugs linked to the phenomenon. There will also be a brief discussion of the clinical or pharmacokinetic consequences of CYP inactivation with regard to drug interaction and toxicity risk.Gaining knowledge about the selective inactivation of CYPs by common therapeutic drugs helps with the assessment of factors that affect the systemic clearance of co-administered drugs and improves comprehension of anticipated interactions with other drugs or xenobiotics.
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Affiliation(s)
- Boon Hooi Tan
- Division of Applied Biomedical Sciences and Biotechnology, International Medical University, Kuala Lumpur, Malaysia
| | - Nafees Ahemad
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Selangor, Malaysia
| | - Yan Pan
- Department of Biomedical Science, University of Nottingham Malaysia Campus, Semenyih, Selangor, Malaysia
| | - Chin Eng Ong
- School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
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2
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Altıntop M, Sağlık Özkan BN, Özdemir A. Design, Synthesis, and Evaluation of New Pyrazolines As Small Molecule Inhibitors of Acetylcholinesterase. ACS OMEGA 2024; 9:31401-31409. [PMID: 39072133 PMCID: PMC11270571 DOI: 10.1021/acsomega.3c10490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/15/2024] [Accepted: 04/23/2024] [Indexed: 07/30/2024]
Abstract
In pursuit of identifying small molecule inhibitors of acetylcholinesterase (AChE), the synthesis of new 2-pyrazolines was performed efficiently. A modified spectrophotometric method was used to examine their inhibitory effects on AChE as well as butyrylcholinesterase. Four compounds (2a, 2g, 2j, and 2l) were identified as selective AChE inhibitors. Molecular docking studies were conducted to explore their potential interactions with the active site of AChE (PDB code: 4EY7). 1-(3-Nitrophenyl)-3-(thiophen-3-yl)-5-[4-(4-morpholinyl)phenyl]-2-pyrazoline (2l) exerted significant AChE inhibitory action with an IC50 value of 0.040 μM close to donepezil (IC50 = 0.021 μM). In addition to π-π interactions with Tyr341, Tyr124, and Trp86 residues, compound 2l was also capable of forming two hydrogen bonds and a salt bridge at the active site of AChE thanks to its nitro group at the meta position of the phenyl moiety linked to the N 1 position of the pyrazoline scaffold. The higher inhibitory effect of compound 2l on AChE when compared to other compounds in this series might be explained by these additional interactions. Based on the in vitro parallel artificial membrane permeability assay, compound 2l was found to have high blood-brain barrier permeability. In vitro and in silico studies suggest that compound 2l is a potent inhibitor of AChE, which is an important target for neurodegenerative disorders, particularly Alzheimer's disease.
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Affiliation(s)
- Mehlika
Dilek Altıntop
- Department of Pharmaceutical
Chemistry, Faculty of Pharmacy, Anadolu
University, 26470 Eskişehir, Turkey
| | | | - Ahmet Özdemir
- Department of Pharmaceutical
Chemistry, Faculty of Pharmacy, Anadolu
University, 26470 Eskişehir, Turkey
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3
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Maji S, Debnath B, Panda S, Manna T, Maity A, Dayaramani R, Nath R, Khan SA, Akhtar MJ. Anticancer Potential of the S-Heterocyclic Ring Containing Drugs and its Bioactivation to Reactive Metabolites. Chem Biodivers 2024; 21:e202400473. [PMID: 38723201 DOI: 10.1002/cbdv.202400473] [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: 02/23/2024] [Accepted: 05/08/2024] [Indexed: 06/20/2024]
Abstract
Sulfur-containing heterocyclic derivatives have been disclosed for binding with a wide range of cancer-specific protein targets. Various interesting derivatives of sulfur-containing heterocyclics such as benzothiazole, thiazole, thiophene, thiazolidinedione, benzothiophene, and phenothiazine, etc have been shown to inhibit diverse signaling pathways implicated in cancer. Significant progress has also been made in molecular targeted therapy against specific enzymes such as kinase receptors due to potential binding interactions inside the ATP pocket. Sulfur-containing heterocyclic ring metal complexes i. e., benzothiazole, thiazole, thiophene, benzothiophene and phenothiazines are among the most promising active anticancer compounds. However, sulfur heteroaromatic rings, particularly thiophene, are of high structural alert due to their metabolism to reactive metabolites. The mere presence of a structural alert itself does not determine compound toxicity therefore, this review focuses on some specific findings that shed light on factors influencing the toxicity. In the current review, synthetic strategies of introducing the sulfur core ring in the synthesized derivatives are discussed with their structure-activity relationships to enhance our understanding of toxicity mechanisms and develop safer therapeutic options. The sulfur-containing marketed anticancer drugs included in this review direct the synthesis of novel compounds and will help in the development of potent, safer sulfur-based anticancer drugs in near future.
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Affiliation(s)
- Sumit Maji
- Department of Pharmacy, Bharat Technology, Uluberia-711316, Howrah, West Bengal, India
| | - Biplab Debnath
- Department of Pharmacy, Bharat Technology, Uluberia-711316, Howrah, West Bengal, India
| | - Shambo Panda
- Department of Pharmacy, Bharat Technology, Uluberia-711316, Howrah, West Bengal, India
| | - Tanusree Manna
- Department of Pharmacy, Bharat Technology, Uluberia-711316, Howrah, West Bengal, India
| | - Arindam Maity
- JIS University, Agarpara Campus, Kolkata-81, Nilgunj Road, Agarpara, Kolkata-700109, India
| | - Richa Dayaramani
- Silver Oak Institute of Pharmacy and Research, Silver Oak University, Ahmedabad, India
| | - Rajarshi Nath
- Department of Pharmacy, Bharat Technology, Uluberia-711316, Howrah, West Bengal, India
- JIS University, Agarpara Campus, Kolkata-81, Nilgunj Road, Agarpara, Kolkata-700109, India
| | - Shah Alam Khan
- Department of Pharmaceutical Chemistry, National University of Science and Technology, PO 620, PC 130, Azaiba, Bousher, Muscat, Sultanate of Oman
| | - Md Jawaid Akhtar
- Department of Pharmaceutical Chemistry, National University of Science and Technology, PO 620, PC 130, Azaiba, Bousher, Muscat, Sultanate of Oman
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4
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Hu XM, Hou YY, Teng XR, Liu Y, Li Y, Li W, Li Y, Ai CZ. Prediction of cytochrome P450-mediated bioactivation using machine learning models and in vitro validation. Arch Toxicol 2024; 98:1457-1467. [PMID: 38492097 DOI: 10.1007/s00204-024-03701-w] [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: 11/16/2023] [Accepted: 01/31/2024] [Indexed: 03/18/2024]
Abstract
Cytochrome P450 (P450)-mediated bioactivation, which can lead to the hepatotoxicity through the formation of reactive metabolites (RMs), has been regarded as the major problem of drug failures. Herein, we purposed to establish machine learning models to predict the bioactivation of P450. On the basis of the literature-derived bioactivation dataset, models for Benzene ring, Nitrogen heterocycle and Sulfur heterocycle were developed with machine learning methods, i.e., Random Forest, Random Subspace, SVM and Naïve Bayes. The models were assessed by metrics like "Precision", "Recall", "F-Measure", "AUC" (Area Under the Curve), etc. Random Forest algorithms illustrated the best predictability, with nice AUC values of 0.949, 0.973 and 0.958 for the test sets of Benzene ring, Nitrogen heterocycle and Sulfur heterocycle models, respectively. 2D descriptors like topological indices, 2D autocorrelations and Burden eigenvalues, etc. contributed most to the models. Furthermore, the models were applied to predict the occurrence of bioactivation of an external verification set. Drugs like selpercatinib, glafenine, encorafenib, etc. were predicted to undergo bioactivation into toxic RMs. In vitro, IC50 shift experiment was performed to assess the potential of bioactivation to validate the prediction. Encorafenib and tirbanibulin were observed of bioactivation potential with shifts of 3-6 folds or so. Overall, this study provided a reliable and robust strategy to predict the P450-mediated bioactivation, which will be helpful to the assessment of adverse drug reactions (ADRs) in clinic and the design of new candidates with lower toxicities.
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Affiliation(s)
- Xin-Man Hu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Yan-Yao Hou
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Xin-Ru Teng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Yong Liu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, 2 Dagong Road, Panjin, 124221, People's Republic of China
| | - Yu Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, People's Republic of China
| | - Wei Li
- Translational Medicine Research Institute, College of Medicine, Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, 136 Jiangyangzhong Road, Yangzhou, 225001, People's Republic of China.
| | - Yan Li
- Department of Materials Science and Chemical Engineering, Dalian University of Technology, Dalian, 116023, Liaoning, People's Republic of China
| | - Chun-Zhi Ai
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, People's Republic of China.
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5
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Farajpour B, Heydarzadeh R, Hussain FHS, Notash B, Mirzaei P, Shiri M. Three-Component Reaction between 3-Acetylcoumarins, Amines, and Elemental Sulfur: A Designed Approach to 3-Amino-4 H-thieno[3,2- c]coumarins. J Org Chem 2024; 89:4375-4383. [PMID: 38470427 DOI: 10.1021/acs.joc.3c02406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
In this work, a series of novel 3-amino-4H-thieno[3,2-c]coumarins were designed and synthesized by a one-pot, catalyst-free, and three-component reaction of 3-acetylcoumarins with amines and elemental sulfur. Readily available starting materials, simple heating conditions, facile installation of a sulfur atom into the molecule using S8 as a sulfur source, acceptable functional group tolerance, and synthetically useful yields are some highlighted benefits of this process.
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Affiliation(s)
- Behnaz Farajpour
- Department of Organic Chemistry, Faculty of Chemistry, Alzahra University, Vanak, Tehran 1993893973, Iran
| | - Roujin Heydarzadeh
- Department of Organic Chemistry, Faculty of Chemistry, Alzahra University, Vanak, Tehran 1993893973, Iran
| | - Faiq H S Hussain
- Medical Analysis Department, Applied Science Faculty, Tishk International University, Erbil 44001, Kurdistan Region, Iraq
| | - Behrouz Notash
- Department of Inorganic Chemistry, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Peiman Mirzaei
- Department of Organic Chemistry, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Morteza Shiri
- Department of Organic Chemistry, Faculty of Chemistry, Alzahra University, Vanak, Tehran 1993893973, Iran
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6
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Tan B, Zhang X, Ansari A, Jadhav P, Tan H, Li K, Chopra A, Ford A, Chi X, Ruiz FX, Arnold E, Deng X, Wang J. Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model. Science 2024; 383:1434-1440. [PMID: 38547259 DOI: 10.1126/science.adm9724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/22/2024] [Indexed: 04/02/2024]
Abstract
The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PLpro) is a promising but challenging drug target. We designed and synthesized 85 noncovalent PLpro inhibitors that bind to a recently discovered ubiquitin binding site and the known BL2 groove pocket near the S4 subsite. Leads inhibited PLpro with the inhibitory constant Ki values from 13.2 to 88.2 nanomolar. The co-crystal structures of PLpro with eight leads revealed their interaction modes. The in vivo lead Jun12682 inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC50 from 0.44 to 2.02 micromolar. Oral treatment with Jun12682 improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting that PLpro inhibitors are promising oral SARS-CoV-2 antiviral candidates.
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Affiliation(s)
- Bin Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xiaoming Zhang
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ahmadullah Ansari
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Prakash Jadhav
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kan Li
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ashima Chopra
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Alexandra Ford
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Xiang Chi
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xufang Deng
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK 74078, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
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7
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Singh A, Ottavi S, Krieger I, Planck K, Perkowski A, Kaneko T, Davis AM, Suh C, Zhang D, Goullieux L, Alex A, Roubert C, Gardner M, Preston M, Smith DM, Ling Y, Roberts J, Cautain B, Upton A, Cooper CB, Serbina N, Tanvir Z, Mosior J, Ouerfelli O, Yang G, Gold BS, Rhee KY, Sacchettini JC, Fotouhi N, Aubé J, Nathan C. Redirecting raltitrexed from cancer cell thymidylate synthase to Mycobacterium tuberculosis phosphopantetheinyl transferase. SCIENCE ADVANCES 2024; 10:eadj6406. [PMID: 38489355 PMCID: PMC10942122 DOI: 10.1126/sciadv.adj6406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024]
Abstract
There is a compelling need to find drugs active against Mycobacterium tuberculosis (Mtb). 4'-Phosphopantetheinyl transferase (PptT) is an essential enzyme in Mtb that has attracted interest as a potential drug target. We optimized a PptT assay, used it to screen 422,740 compounds, and identified raltitrexed, an antineoplastic antimetabolite, as the most potent PptT inhibitor yet reported. While trying unsuccessfully to improve raltitrexed's ability to kill Mtb and remove its ability to kill human cells, we learned three lessons that may help others developing antibiotics. First, binding of raltitrexed substantially changed the configuration of the PptT active site, complicating molecular modeling of analogs based on the unliganded crystal structure or the structure of cocrystals with inhibitors of another class. Second, minor changes in the raltitrexed molecule changed its target in Mtb from PptT to dihydrofolate reductase (DHFR). Third, the structure-activity relationship for over 800 raltitrexed analogs only became interpretable when we quantified and characterized the compounds' intrabacterial accumulation and transformation.
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Affiliation(s)
- Amrita Singh
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - Samantha Ottavi
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Inna Krieger
- Department of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX 77843, USA
| | - Kyle Planck
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Andrew Perkowski
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, New York, NY 10005, USA
| | | | - Christine Suh
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - David Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | | | - Alexander Alex
- AMG Consultants Limited, Camburgh House, 27 New Dover Road, Canterbury, Kent, CT1 3DN, UK
- Evenor Consulting Limited, The New Barn, Mill Lane, Eastry, Kent CT13 0JW, UK
| | | | - Mark Gardner
- AMG Consultants Limited, Camburgh House, 27 New Dover Road, Canterbury, Kent, CT1 3DN, UK
| | - Marian Preston
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Dave M. Smith
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Yan Ling
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - Julia Roberts
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - Bastien Cautain
- Evotec ID (Lyon), SAS 40 Avenue Tony Garnier, Lyon 69001, France
| | - Anna Upton
- Evotec ID (Lyon), SAS 40 Avenue Tony Garnier, Lyon 69001, France
| | | | - Natalya Serbina
- Global Alliance for TB Drug Development, New York, NY 10005, USA
| | - Zaid Tanvir
- Global Alliance for TB Drug Development, New York, NY 10005, USA
| | - John Mosior
- Department of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX 77843, USA
| | - Ouathek Ouerfelli
- Organic Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Guangli Yang
- Organic Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ben S. Gold
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - Kyu Y. Rhee
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX 77843, USA
| | - Nader Fotouhi
- Global Alliance for TB Drug Development, New York, NY 10005, USA
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
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8
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Canale V, Skiba-Kurek I, Klesiewicz K, Papież M, Ropek M, Pomierny B, Piska K, Koczurkiewicz-Adamczyk P, Empel J, Karczewska E, Zajdel P. Improving Activity of New Arylurea Agents against Multidrug-Resistant and Biofilm-Producing Staphylococcus epidermidis. ACS Med Chem Lett 2024; 15:369-375. [PMID: 38505856 PMCID: PMC10945555 DOI: 10.1021/acsmedchemlett.3c00536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 03/21/2024] Open
Abstract
Multidrug-resistant (MDR) strains of Staphylococcus epidermidis (S. epidermidis), prevalent in hospital environments, contribute to increased morbidity and mortality, especially among newborns, posing a critical concern for neonatal sepsis. In response to the pressing demand for novel antibacterial therapies, we present findings from synthetic chemistry and structure-activity relationship studies focused on arylsulfonamide/arylurea derivatives of aryloxy[1-(thien-2-yl)propyl]piperidines. Through bioisosteric replacement of the sulfonamide fragment with a urea moiety, compound 25 was identified, demonstrating potent bacteriostatic activity against clinical multidrug-resistant S. epidermidis strains (MIC50 and MIC90 = 1.6 and 3.125 μg/mL). Importantly, it showed activity against linezolid-resistant strains and exhibited selectivity over mammalian cells. Compound 25 displayed antibiofilm-forming properties against clinical S. epidermidis strains and demonstrated the capacity to eliminate existing biofilm layers. Additionally, it induced complete depolarization of the bacterial membrane in clinical S. epidermidis strains. In light of these findings, targeting bacterial cell membranes with compound 25 emerges as a promising strategy in the fight against multidrug-resistant S. epidermidis strains.
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Affiliation(s)
- Vittorio Canale
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Iwona Skiba-Kurek
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Karolina Klesiewicz
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Monika Papież
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Marlena Ropek
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Bartosz Pomierny
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Kamil Piska
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | | | - Joanna Empel
- Department
of Epidemiology and Clinical Microbiology, National Medicines Institute, 30/34 Chełmska Street, 00-725 Warsaw, Poland
| | - Elżbieta Karczewska
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Paweł Zajdel
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
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9
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Liu T, Padyana AK, Judd ET, Jin L, Hammoudeh D, Kung C, Dang L. Structure-Based Design of AG-946, a Pyruvate Kinase Activator. ChemMedChem 2024; 19:e202300559. [PMID: 38109501 DOI: 10.1002/cmdc.202300559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
Pyruvate kinase (PK) is the enzyme that catalyzes the conversion of phosphoenolpyruvate and adenosine diphosphate to pyruvate and adenosine triphosphate in glycolysis and plays a crucial role in regulating cell metabolism. We describe the structure-based design of AG-946, an activator of PK isoforms, including red blood cell-specific forms of PK (PKR). This was designed to have a pseudo-C2-symmetry matching its allosteric binding site on the PK enzyme, which increased its potency toward PKR while reducing activity against off-targets observed from the original scaffold. AG-946 (1) demonstrated activation of human wild-type PK (half-maximal activation concentration [AC50 ]=0.005 μM) and a panel of mutated PK proteins (K410E [AC50 =0.0043 μM] and R510Q [AC50 =0.0069 μM]), (2) displayed a significantly longer half-time of activation (>150-fold) compared with 6-(3-methoxybenzyl)-4-methyl-2-(methylsulfinyl)-4,6-dihydro-5H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin-5-one, and (3) stabilized PKR R510Q, an unstable mutant PKR enzyme, and preserved its catalytic activity under increasingly denaturing conditions. As a potent, oral, small-molecule allosteric activator of wild-type and mutant PKR, AG-946 was advanced to human clinical trials.
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Affiliation(s)
- Tao Liu
- Ensem Therapeutics, 880 Winter St, Waltham, MA 02451, USA
| | | | - Evan T Judd
- Novartis Institute for Biomedical Research, 250 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Lei Jin
- Agios Pharmaceuticals, Inc., 88 Sidney St, Cambridge, MA, USA
| | - Dalia Hammoudeh
- Agios Pharmaceuticals Inc., 88 Sidney St, Cambridge, MA, USA
| | - Charles Kung
- Remix Therapeutics, 100 Forge Rd, Watertown, MA 02472, USA
| | - Lenny Dang
- Verolix, Inc., 800 Boylston St. Unit 900147, Boston, MA, 02199, USA
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10
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El-Atawy MA, Hanna DH, Bashal AH, Ahmed HA, Alshammari EM, Hamed EA, Aljohani AR, Omar AZ. Synthesis, Characterization, Antioxidant, and Anticancer Activity against Colon Cancer Cells of Some Cinnamaldehyde-Based Chalcone Derivatives. Biomolecules 2024; 14:216. [PMID: 38397453 PMCID: PMC10886690 DOI: 10.3390/biom14020216] [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: 01/17/2024] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
The purpose of the current investigation was to produce cinammaldehyde-based chalcone derivatives (3a-k) to evaluate their potential effectiveness as antioxidant and inhibitory agents versus human Caco-2 cancer cells. The findings obtained using the DPPH assay showed that compound 3e had the highest effective antioxidant activity with the best IC50 value compared with the other compounds. Moreover, the cytotoxic findings revealed that compound 3e was the best compound for inhibiting Caco-2 development in contrast to all other produced derivatives, with the lowest IC50 concentration (32.19 ± 3.92 µM), and it also had no detrimental effects on healthy human lung cells (wi38 cells). Exposure of Caco-2 cells with this IC50 value of compound 3e resulted in a substantial rise in the number of early and late cells that are apoptotic with a significant comet nucleus when compared with control cells employing the annexin V/PI and comet evaluations, respectively. Furthermore, qRT-PCR and ELISA examinations indicated that compound 3e significantly altered the expression of genes and their relative proteins related to apoptosis in the treated Caco-2 cells, thus significantly inhibiting Caco-2 growth through activating Caspase-3 via an intrinsic apoptotic pathway. As a result, compound 3e could serve as an effective therapy for human colon cancer.
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Affiliation(s)
- Mohamed A. El-Atawy
- Chemistry Department, Faculty of Science at Yanbu, Taibah University, Yanbu 46423, Saudi Arabia; (M.A.E.-A.); (A.H.B.); (H.A.A.); (A.R.A.)
- Chemistry Department, Faculty of Science, Alexandria University, P.O. Box 426 Ibrahemia, Alexandria 21321, Egypt; (E.A.H.); (A.Z.O.)
| | - Demiana H. Hanna
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Ali H. Bashal
- Chemistry Department, Faculty of Science at Yanbu, Taibah University, Yanbu 46423, Saudi Arabia; (M.A.E.-A.); (A.H.B.); (H.A.A.); (A.R.A.)
| | - Hoda A. Ahmed
- Chemistry Department, Faculty of Science at Yanbu, Taibah University, Yanbu 46423, Saudi Arabia; (M.A.E.-A.); (A.H.B.); (H.A.A.); (A.R.A.)
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Eida M. Alshammari
- Department of Chemistry, College of Sciences, University of Ha’il, Ha’il 55473, Saudi Arabia;
| | - Ezzat A. Hamed
- Chemistry Department, Faculty of Science, Alexandria University, P.O. Box 426 Ibrahemia, Alexandria 21321, Egypt; (E.A.H.); (A.Z.O.)
| | - Abdullah R. Aljohani
- Chemistry Department, Faculty of Science at Yanbu, Taibah University, Yanbu 46423, Saudi Arabia; (M.A.E.-A.); (A.H.B.); (H.A.A.); (A.R.A.)
- Saudi Irrigation Organization (SIO), Al-Hassa 31982, Saudi Arabia
| | - Alaa Z. Omar
- Chemistry Department, Faculty of Science, Alexandria University, P.O. Box 426 Ibrahemia, Alexandria 21321, Egypt; (E.A.H.); (A.Z.O.)
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11
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Hikmawanti NPE, Saputri FC, Yanuar A, Jantan I, Ningrum RA, Mun'im A. Insights into the anti-infective effects of Pluchea indica (L.) Less and its bioactive metabolites against various bacteria, fungi, viruses, and parasites. JOURNAL OF ETHNOPHARMACOLOGY 2024; 320:117387. [PMID: 37944874 DOI: 10.1016/j.jep.2023.117387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/12/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Pluchea indica (L.) Less (family Asteraceae) is popularly consumed as a medicinal vegetable and used in ethnomedicine to treat various diseases including gastrointestinal problems such as dysentery and leucorrhoea, which are due to bacterial, fungal or parasitic infections. There have been numerous studies on the antimicrobial effects of the plant due to these ethnomedicine use. AIM OF THIS REVIEW This review is comprehensively discussed the information on the anti-infective properties of P. indica and its secondary metabolites, and highlight the potential of the plant as a new source of anti-infective agents. MATERIALS AND METHODS Scientific databases such as Scopus, Google Scholar, ScienceDirect, PubMed, Wiley Online Library, and ACS Publications were used to gather the relevant information on the ability of P. indica to fight infections, with the leaves and roots receiving most of the attention. RESULTS Anti-bacterial, anti-mycobacterial, anti-malarial, and anti-viral activities have been the most exploited. Most studies were carried out on the crude extracts of the plant and in most studies the bioactive extracts were not standardized or chemically characterized. Several studies have reported the anti-infective activity of several bioactive components of P. indica including caffeoylquinic acids, terpenoid glycosides, thiophenes, and kaempferol. CONCLUSIONS The strong anti-infective effect and underlying mechanisms of the compounds provide insights into the potential of P. indica as a source of new leads for the development of anti-infective agents for use in food and pharmaceutical industries.
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Affiliation(s)
- Ni Putu Ermi Hikmawanti
- Graduate Program of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Indonesia, Cluster of Health Sciences Building, Depok, 16424, West Java, Indonesia; Department of Pharmaceutical Biology, Faculty of Pharmacy and Sciences, Universitas Muhammadiyah Prof. DR. HAMKA, East Jakarta, 13460, DKI Jakarta, Indonesia; National Metabolomics Collaborative Research Center, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, 16424, Indonesia.
| | - Fadlina Chany Saputri
- Department of Pharmacology-Toxicology, Faculty of Pharmacy, Universitas Indonesia, Depok, 16424, West Java, Indonesia; National Metabolomics Collaborative Research Center, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, 16424, Indonesia.
| | - Arry Yanuar
- Department of Biomedical Computation-Drug Design, Faculty of Pharmacy, Universitas Indonesia, Depok, 16424, West Java, Indonesia; National Metabolomics Collaborative Research Center, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, 16424, Indonesia.
| | - Ibrahim Jantan
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia.
| | - Ratih Asmana Ningrum
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Raya Bogor Street KM.46, Cibinong, Bogor, West Java, 16911, Indonesia; National Metabolomics Collaborative Research Center, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, 16424, Indonesia.
| | - Abdul Mun'im
- Department of Pharmacognosy-Phytochemistry, Faculty of Pharmacy, Universitas Indonesia, Cluster of Health Sciences Building, Depok, 16424, West Java, Indonesia; National Metabolomics Collaborative Research Center, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, 16424, Indonesia.
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12
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Yarovaya OI, Filimonov AS, Baev DS, Borisevich SS, Zaykovskaya AV, Chirkova VY, Marenina MK, Meshkova YV, Belenkaya SV, Shcherbakov DN, Gureev MA, Luzina OA, Pyankov OV, Salakhutdinov NF, Khvostov MV. The Potential of Usnic-Acid-Based Thiazolo-Thiophenes as Inhibitors of the Main Protease of SARS-CoV-2 Viruses. Viruses 2024; 16:215. [PMID: 38399993 PMCID: PMC10893357 DOI: 10.3390/v16020215] [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: 11/27/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Although the COVID-19 pandemic caused by SARS-CoV-2 viruses is officially over, the search for new effective agents with activity against a wide range of coronaviruses is still an important task for medical chemists and virologists. We synthesized a series of thiazolo-thiophenes based on (+)- and (-)-usnic acid and studied their ability to inhibit the main protease of SARS-CoV-2. Substances containing unsubstituted thiophene groups or methyl- or bromo-substituted thiophene moieties showed moderate activity. Derivatives containing nitro substituents in the thiophene heterocycle-just as pure (+)- and (-)-usnic acids-showed no anti-3CLpro activity. Kinetic parameters of the most active compound, (+)-3e, were investigated, and molecular modeling of the possible interaction of the new thiazolo-thiophenes with the active site of the main protease was carried out. We evaluated the binding energies of the ligand and protein in a ligand-protein complex. Active compound (+)-3e was found to bind with minimum free energy; the binding of inactive compound (+)-3g is characterized by higher values of minimum free energy; the positioning of pure (+)-usnic acid proved to be unstable and is accompanied by the formation of intermolecular contacts with many amino acids of the catalytic binding site. Thus, the molecular dynamics results were consistent with the experimental data. In an in vitro antiviral assay against six strains (Wuhan, Delta, and four Omicron sublineages) of SARS-CoV-2, (+)-3e demonstrated pronounced antiviral activity against all the strains.
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Affiliation(s)
- Olga I. Yarovaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Aleksandr S. Filimonov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Dmitriy S. Baev
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- Synchrotron Radiation Facility SKIF, G.K. Boreskov Institute of Catalysis SB RAS, 630559 Koltsovo, Russia;
| | - Sophia S. Borisevich
- Synchrotron Radiation Facility SKIF, G.K. Boreskov Institute of Catalysis SB RAS, 630559 Koltsovo, Russia;
- Laboratory of Chemical Physics, Ufa Institute of Chemistry, Ufa Federal Research Centre, 450078 Ufa, Russia
| | - Anna V. Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Varvara Yu. Chirkova
- Institute of Biology and Biotechnology, Altay State University, 656049 Barnaul, Russia;
| | - Mariya K. Marenina
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Yulia V. Meshkova
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Svetlana V. Belenkaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Dmitriy N. Shcherbakov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
- Institute of Biology and Biotechnology, Altay State University, 656049 Barnaul, Russia;
| | - Maxim A. Gureev
- Laboratory of Bio- and Cheminformatics, St. Petersburg School of Physics, Mathematics and Computer Science, HSE University, 194100 St. Peterburg, Russia;
| | - Olga A. Luzina
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Oleg V. Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Mikhail V. Khvostov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
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13
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Velcicky J, Janser P, Gommermann N, Brenneisen S, Ilic S, Vangrevelinghe E, Stiefl N, Boettcher A, Arnold C, Malinverni C, Dawson J, Murgasova R, Desrayaud S, Beltz K, Hinniger A, Dekker C, Farady CJ, Mackay A. Discovery of Potent, Orally Bioavailable, Tricyclic NLRP3 Inhibitors. J Med Chem 2024; 67:1544-1562. [PMID: 38175811 DOI: 10.1021/acs.jmedchem.3c02098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
NLRP3 is a molecular sensor recognizing a wide range of danger signals. Its activation leads to the assembly of an inflammasome that allows for activation of caspase-1 and subsequent maturation of IL-1β and IL-18, as well as cleavage of Gasdermin-d and pyroptotic cell death. The NLRP3 inflammasome has been implicated in a plethora of diseases including gout, type 2 diabetes, atherosclerosis, Alzheimer's disease, and cancer. In this publication, we describe the discovery of a novel, tricyclic, NLRP3-binding scaffold by high-throughput screening. The hit (1) could be optimized into an advanced compound NP3-562 demonstrating excellent potency in human whole blood and full inhibition of IL-1β release in a mouse acute peritonitis model at 30 mg/kg po dose. An X-ray structure of NP3-562 bound to the NLRP3 NACHT domain revealed a unique binding mode as compared to the known sulfonylurea-based inhibitors. In addition, NP3-562 shows also a good overall development profile.
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Affiliation(s)
- Juraj Velcicky
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | - Philipp Janser
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | | | | | - Slavica Ilic
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | | | | | | | | | | | - Janet Dawson
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | | | | | - Karen Beltz
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | | | - Carien Dekker
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
| | | | - Angela Mackay
- Novartis Biomedical Research, CH-4002 Basel, Switzerland
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14
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Klug DM, Tse EG, Silva DG, Cao Y, Charman SA, Chauhan J, Crighton E, Dichiara M, Drake C, Drewry D, da Silva Emery F, Ferrins L, Graves L, Hopkins E, Kresina TAC, Lorente-Macías Á, Perry B, Phipps R, Quiroga B, Quotadamo A, Sabatino GN, Sama A, Schätzlein A, Simpson QJ, Steele J, Shanu-Wilson J, Sjö P, Stapleton P, Swain CJ, Vaideanu A, Xie H, Zuercher W, Todd MH. Open Source Antibiotics: Simple Diarylimidazoles Are Potent against Methicillin-Resistant Staphylococcus aureus. ACS Infect Dis 2023; 9:2423-2435. [PMID: 37991879 PMCID: PMC10714399 DOI: 10.1021/acsinfecdis.3c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/24/2023]
Abstract
Antimicrobial resistance (AMR) is widely acknowledged as one of the most serious public health threats facing the world, yet the private sector finds it challenging to generate much-needed medicines. As an alternative discovery approach, a small array of diarylimidazoles was screened against the ESKAPE pathogens, and the results were made publicly available through the Open Source Antibiotics (OSA) consortium (https://github.com/opensourceantibiotics). Of the 18 compounds tested (at 32 μg/mL), 15 showed >90% growth inhibition activity against methicillin-resistant Staphylococcus aureus (MRSA) alone. In the subsequent hit-to-lead optimization of this chemotype, 147 new heterocyclic compounds containing the diarylimidazole and other core motifs were synthesized and tested against MRSA, and their structure-activity relationships were identified. While potent, these compounds have moderate to high intrinsic clearance and some associated toxicity. The best overall balance of parameters was found with OSA_975, a compound with good potency, good solubility, and reduced intrinsic clearance in rat hepatocytes. We have progressed toward the knowledge of the molecular target of these phenotypically active compounds, with proteomic techniques suggesting TGFBR1 is potentially involved in the mechanism of action. Further development of these compounds toward antimicrobial medicines is available to anyone under the licensing terms of the project.
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Affiliation(s)
- Dana M. Klug
- School
of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Edwin G. Tse
- School
of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Daniel G. Silva
- School
of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
- School
of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903. Brazil
| | - Yafeng Cao
- WuXi
AppTec (Wuhan) Co., Ltd., 666 Gaoxin Road, East Lake High-Tech Development Zone, Wuhan 430075, People’s Republic of China
| | - Susan A. Charman
- Centre
for Drug Candidate Optimization, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Jyoti Chauhan
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Elly Crighton
- Centre
for Drug Candidate Optimization, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Maria Dichiara
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Chris Drake
- Hypha Discovery, 154b Brook Dr, Milton, Abingdon OX14 4SD, United Kingdom
| | - David Drewry
- UNC Lineberger
Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Flavio da Silva Emery
- School
of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903. Brazil
| | - Lori Ferrins
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Lee Graves
- Department
of Pharmacology, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Emily Hopkins
- Hypha Discovery, 154b Brook Dr, Milton, Abingdon OX14 4SD, United Kingdom
| | - Thomas A. C. Kresina
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Álvaro Lorente-Macías
- Department
of Pharmacology, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department
of Medicinal & Organic Chemistry and Excellence Research Unit
of ‘‘Chemistry Applied to Biomedicine and the Environment’’,
Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain
- A. L-M.
Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh EH4 2XR, United Kingdom
| | - Benjamin Perry
- Drugs
for Neglected Diseases initiative (DNDi), 15 Chemin Camille-Vidart, 1202 Geneva, Switzerland
| | - Richard Phipps
- Hypha Discovery, 154b Brook Dr, Milton, Abingdon OX14 4SD, United Kingdom
| | - Bruno Quiroga
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Antonio Quotadamo
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
- Clinical
and Experimental Medicine PhD Program, University
of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Giada N. Sabatino
- School
of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Anthony Sama
- Citizen
scientist, New York, New York 11570, United States
| | - Andreas Schätzlein
- School
of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Quillon J. Simpson
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Jonathan Steele
- Hypha Discovery, 154b Brook Dr, Milton, Abingdon OX14 4SD, United Kingdom
| | - Julia Shanu-Wilson
- Hypha Discovery, 154b Brook Dr, Milton, Abingdon OX14 4SD, United Kingdom
| | - Peter Sjö
- Drugs
for Neglected Diseases initiative (DNDi), 15 Chemin Camille-Vidart, 1202 Geneva, Switzerland
| | - Paul Stapleton
- School
of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Christopher J. Swain
- Cambridge
MedChem Consulting, 8
Mangers Lane, Duxford, Cambridge CB22 4RN, United Kingdom
| | - Alexandra Vaideanu
- School
of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Huanxu Xie
- WuXi
AppTec (Wuhan) Co., Ltd., 666 Gaoxin Road, East Lake High-Tech Development Zone, Wuhan 430075, People’s Republic of China
| | - William Zuercher
- UNC Lineberger
Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Matthew H. Todd
- School
of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
- Structural
Genomics Consortium, University College
London, 29-39 Brunswick
Square, London WC1N 1AX, United Kingdom
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15
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Abel SAG, Alnafta N, Asmus E, Bollenbach-Wahl B, Braun R, Dittgen J, Endler A, Frackenpohl J, Freigang J, Gatzweiler E, Heinemann I, Helmke H, Laber B, Lange G, Machettira A, McArthur G, Müller T, Odaybat M, Reingruber AM, Roth S, Rosinger CH, Schmutzler D, Schulte W, Stoppel R, Tiebes J, Volpin G, Barber DM. A Study in Scaffold Hopping: Discovery and Optimization of Thiazolopyridines as Potent Herbicides That Inhibit Acyl-ACP Thioesterase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18212-18226. [PMID: 37677080 DOI: 10.1021/acs.jafc.3c02490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
In the search for new chemical entities that can control resistant weeds by addressing novel modes of action (MoAs), we were interested in further exploring a compound class that contained a 1,8-naphthyridine core. By leveraging scaffold hopping methodologies, we were able to discover the new thiazolopyridine compound class that act as potent herbicidal molecules. Further biochemical investigations allowed us to identify that the thiazolopyridines inhibit acyl-acyl carrier protein (ACP) thioesterase (FAT), with this being further confirmed via an X-ray cocrystal structure. Greenhouse trials revealed that the thiazolopyridines display excellent control of grass weed species in pre-emergence application coupled with dose response windows that enable partial selectivity in certain crops.
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Affiliation(s)
- Steven A G Abel
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Neanne Alnafta
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Elisabeth Asmus
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Birgit Bollenbach-Wahl
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Ralf Braun
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Jan Dittgen
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Anne Endler
- Targenomix GmbH, Am Mühlenberg 11, 14476, Potsdam, Germany
| | - Jens Frackenpohl
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Jörg Freigang
- Research and Development, Hit Discovery, Bayer AG, Crop Science Division, Alfred-Nobel-Straße 50, 40789, Monheim am Rhein, Germany
| | - Elmar Gatzweiler
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Ines Heinemann
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Hendrik Helmke
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Bernd Laber
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Gudrun Lange
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Anu Machettira
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Gillian McArthur
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Thomas Müller
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Magdalena Odaybat
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Anna M Reingruber
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Sina Roth
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Christopher H Rosinger
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Dirk Schmutzler
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Wolfgang Schulte
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Rhea Stoppel
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Jörg Tiebes
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Giulio Volpin
- Research and Development, Small Molecules Technologies, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - David M Barber
- Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
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16
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M. S, V. J, Ahmad SF, Attia SM, Emran TB, Patil RB, Ahmed SSSJ. Structural Characteristics of PON1 with Leu55Met and Gln192Arg Variants Influencing Oxidative-Stress-Related Diseases: An Integrated Molecular Modeling and Dynamics Study. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:2060. [PMID: 38138163 PMCID: PMC10744641 DOI: 10.3390/medicina59122060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/04/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023]
Abstract
Background and Objectives: PON1 is a multi-functional antioxidant protein that hydrolyzes a variety of endogenous and exogenous substrates in the human system. Growing evidence suggests that the Leu55Met and Gln192Arg substitutions alter PON1 activity and are linked with a variety of oxidative-stress-related diseases. Materials and Methods: We implemented structural modeling and molecular dynamics (MD) simulation along with essential dynamics of PON1 and molecular docking with their endogenous (n = 4) and exogenous (n = 6) substrates to gain insights into conformational changes and binding affinity in order to characterize the specific functional ramifications of PON1 variants. Results: The Leu55Met variation had a higher root mean square deviation (0.249 nm) than the wild type (0.216 nm) and Gln192Arg (0.202 nm), implying increased protein flexibility. Furthermore, the essential dynamics analysis confirms the structural change in PON1 with Leu55Met vs. Gln192Arg and wild type. Additionally, PON1 with Leu55Met causes local conformational alterations at the substrate binding site, leading to changes in binding affinity with their substrates. Conclusions: Our findings highlight the structural consequences of the variants, which would increase understanding of the role of PON1 in the pathogenesis of oxidative-stress-related diseases, as well as the management of endogenous and exogenous chemicals in the treatment of diseases.
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Affiliation(s)
- Sudhan M.
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India
| | - Janakiraman V.
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India
| | - Sheikh F. Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sabry M. Attia
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Rajesh B. Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Societys, Sinhgad College of Pharmacy, Vadgaon (BK), Pune 411041, Maharashtra, India
| | - Shiek S. S. J. Ahmed
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India
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17
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Qunies AM, Spitznagel BD, Du Y, David Weaver C, Emmitte KA. Design, synthesis, and biological evaluation of a novel series of 1,2,4-oxadiazole inhibitors of SLACK potassium channels: Identification of in vitro tool VU0935685. Bioorg Med Chem 2023; 95:117487. [PMID: 37812884 PMCID: PMC10842602 DOI: 10.1016/j.bmc.2023.117487] [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: 07/05/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/11/2023]
Abstract
Malignant migrating partial seizure of infancy (MMPSI) is a devastating and pharmacoresistant form of infantile epilepsy. MMPSI has been linked to multiple gain-of-function (GOF) mutations in the KCNT1 gene, which encodes for a potassium channel often referred to as SLACK. SLACK channels are sodium-activated potassium channels distributed throughout the central nervous system (CNS) and the periphery. The investigation described here aims to discover SLACK channel inhibitor tool compounds and profile their pharmacokinetic and pharmacodynamic properties. A SLACK channel inhibitor VU0531245 (VU245) was identified via a high-throughput screen (HTS) campaign. Structure-activity relationship (SAR) studies were conducted in five distinct regions of the hit VU245. VU245 analogs were evaluated for their ability to affect SLACK channel activity using a thallium flux assay in HEK-293 cells stably expressing wild-type (WT) human SLACK. Selected analogs were tested for metabolic stability in mouse liver microsomes and plasma-protein binding in mouse plasma. The same set of analogs was tested via thallium flux for activity versus human A934T SLACK and other structurally related potassium channels, including SLICK and Maxi-K. In addition, potencies for selected VU245 analogs were obtained using whole-cell electrophysiology (EP) assays in CHO cells stably expressing WT human SLACK through an automated patch clamp system. Results revealed that this scaffold tolerates structural changes in some regions, with some analogs demonstrating improved SLACK inhibitory activity, good selectivity against the other channels tested, and modest improvements in metabolic clearance. Analog VU0935685 represents a new, structurally distinct small-molecule inhibitor of SLACK channels that can serve as an in vitro tool for studying this target.
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Affiliation(s)
- Alshaima'a M Qunies
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | | | - Yu Du
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - C David Weaver
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Kyle A Emmitte
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA.
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18
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Badshah G, Gomes CMB, Ali S, Luz EQ, Silvério GL, Santana FS, Seckler D, Paixão DB, Schneider PH, Rampon DS. Palladium-Catalyzed Direct Selanylation of Chalcogenophenes and Arenes Assisted by 2-(Methylthio)amide. J Org Chem 2023; 88:14033-14047. [PMID: 37712931 DOI: 10.1021/acs.joc.3c01577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
The direct and selective conversion of a C-H bond into a C-Se bond remains a significant challenge, which is even more intricate with substrates having an innate regioselectivity under several reaction conditions, such as chalcogenophenes. We overrode their selectivity toward selanylation using palladium, copper, and the 2-(methylthio)amide directing group. This chelation-assisted direct selanylation was also suitable for mono and double ortho functionalization of arenes. The mechanistic studies indicate high-valent Pd(IV) species in the catalytic cycle, a reversible C-H activation step, and Cu(II) as a sequestering agent for organoselenide byproducts.
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Affiliation(s)
- Gul Badshah
- Laboratory of Polymers and Catalysis(LaPoCa),Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-980, Paraná, Brazil
| | - Carla M B Gomes
- Laboratory of Polymers and Catalysis(LaPoCa),Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-980, Paraná, Brazil
| | - Sher Ali
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, São Paulo, Brazil
| | - Eduardo Q Luz
- Laboratory of Polymers and Catalysis(LaPoCa),Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-980, Paraná, Brazil
| | - Gabriel L Silvério
- Laboratory of Polymers and Catalysis(LaPoCa),Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-980, Paraná, Brazil
| | - Francielli S Santana
- Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-990, Paraná, Brazil
| | - Diego Seckler
- Laboratory of Polymers and Catalysis(LaPoCa),Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-980, Paraná, Brazil
| | - Douglas B Paixão
- Instituto de Química, Departamento de Química Orgânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Rio Grande do Sul, Brazil
| | - Paulo H Schneider
- Instituto de Química, Departamento de Química Orgânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Rio Grande do Sul, Brazil
| | - Daniel S Rampon
- Laboratory of Polymers and Catalysis(LaPoCa),Department of Chemistry, Federal University of Paraná, P.O. Box 19061, Curitiba 81531-980, Paraná, Brazil
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19
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A Varon H, Santos P, Lopez-Vallejo F, Y Soto C. Novel scaffolds targeting Mycobacterium tuberculosis plasma membrane Ca 2+ transporter CtpF by structure-based strategy. Bioorg Chem 2023; 138:106648. [PMID: 37315451 DOI: 10.1016/j.bioorg.2023.106648] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/20/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
CtpF is a Ca2+ transporter P-type ATPase key to the response to stress conditions and to Mycobacterium tuberculosis virulence, therefore, an interesting target for the design of novel anti-Mtb compounds. In this work, molecular dynamics simulations of four previously identified CtpF inhibitors allowed recognizing the key protein-ligand (P-L) interactions, which were then used to perform a pharmacophore-based virtual screening (PBVS) of 22 million compounds from ZINCPharmer. The top-rated compounds were then subjected to molecular docking, and their scores were refined by MM-GBSA calculations. In vitro assays showed that ZINC04030361 (Compound 7) was the best promising candidate, showing a MIC of 25.0 μg/mL, inhibition of Ca2+-ATPase activity (IC50) of 3.3 μM, cytotoxic activity of 27.2 %, and hemolysis of red blood cells lower than 0.2 %. Interestingly, the ctpF gene is upregulated in the presence of compound 7, compared to other alkali/alkaline P-type ATPases coding genes, strongly suggesting that CtpF is a compound 7-specific target.
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Affiliation(s)
- Henry A Varon
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 30 N° 45-03, Bogotá, Colombia
| | - Paola Santos
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 30 N° 45-03, Bogotá, Colombia
| | - Fabian Lopez-Vallejo
- Departamento de Física y Química, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Colombia-Sede Manizales, Kilómetro 9 vía al aeropuerto, La Nubia, Manizales 170003, Colombia.
| | - Carlos Y Soto
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 30 N° 45-03, Bogotá, Colombia
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20
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Riley CM, Elwood JML, Henry MC, Hunter I, Daniel Lopez-Fernandez J, McEwan IJ, Jamieson C. Current and emerging approaches to noncompetitive AR inhibition. Med Res Rev 2023; 43:1701-1747. [PMID: 37062876 DOI: 10.1002/med.21961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 04/18/2023]
Abstract
The androgen receptor (AR) has been shown to be a key determinant in the pathogenesis of castration-resistant prostate cancer (CRPC). The current standard of care therapies targets the ligand-binding domain of the receptor and can afford improvements to life expectancy often only in the order of months before resistance occurs. Emerging preclinical and clinical compounds that inhibit receptor activity via differentiated mechanisms of action which are orthogonal to current antiandrogens show promise for overcoming treatment resistance. In this review, we present an authoritative summary of molecules that noncompetitively target the AR. Emerging small molecule strategies for targeting alternative domains of the AR represent a promising area of research that shows significant potential for future therapies. The overall quality of lead candidates in the area of noncompetitive AR inhibition is discussed, and it identifies the key chemotypes and associated properties which are likely to be, or are currently, positioned to be first in human applications.
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Affiliation(s)
- Christopher M Riley
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Jessica M L Elwood
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Martyn C Henry
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Irene Hunter
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Iain J McEwan
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Craig Jamieson
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
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21
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Du BX, Long Y, Li X, Wu M, Shi JY. CMMS-GCL: cross-modality metabolic stability prediction with graph contrastive learning. Bioinformatics 2023; 39:btad503. [PMID: 37572298 PMCID: PMC10457661 DOI: 10.1093/bioinformatics/btad503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/26/2023] [Accepted: 08/11/2023] [Indexed: 08/14/2023] Open
Abstract
MOTIVATION Metabolic stability plays a crucial role in the early stages of drug discovery and development. Accurately modeling and predicting molecular metabolic stability has great potential for the efficient screening of drug candidates as well as the optimization of lead compounds. Considering wet-lab experiment is time-consuming, laborious, and expensive, in silico prediction of metabolic stability is an alternative choice. However, few computational methods have been developed to address this task. In addition, it remains a significant challenge to explain key functional groups determining metabolic stability. RESULTS To address these issues, we develop a novel cross-modality graph contrastive learning model named CMMS-GCL for predicting the metabolic stability of drug candidates. In our framework, we design deep learning methods to extract features for molecules from two modality data, i.e. SMILES sequence and molecule graph. In particular, for the sequence data, we design a multihead attention BiGRU-based encoder to preserve the context of symbols to learn sequence representations of molecules. For the graph data, we propose a graph contrastive learning-based encoder to learn structure representations by effectively capturing the consistencies between local and global structures. We further exploit fully connected neural networks to combine the sequence and structure representations for model training. Extensive experimental results on two datasets demonstrate that our CMMS-GCL consistently outperforms seven state-of-the-art methods. Furthermore, a collection of case studies on sequence data and statistical analyses of the graph structure module strengthens the validation of the interpretability of crucial functional groups recognized by CMMS-GCL. Overall, CMMS-GCL can serve as an effective and interpretable tool for predicting metabolic stability, identifying critical functional groups, and thus facilitating the drug discovery process and lead compound optimization. AVAILABILITY AND IMPLEMENTATION The code and data underlying this article are freely available at https://github.com/dubingxue/CMMS-GCL.
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Affiliation(s)
- Bing-Xue Du
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
- Institute for Infocomm Research (IR), Agency for Science, Technology and Research (A*STAR), Singapore 138632, Singapore
| | - Yahui Long
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore
| | - Xiaoli Li
- Institute for Infocomm Research (IR), Agency for Science, Technology and Research (A*STAR), Singapore 138632, Singapore
| | - Min Wu
- Institute for Infocomm Research (IR), Agency for Science, Technology and Research (A*STAR), Singapore 138632, Singapore
| | - Jian-Yu Shi
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
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22
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Apaza Ticona L, Sánchez Sánchez-Corral J, Flores Sepúlveda A, Soriano Vázquez C, Hernán Vieco C, Rumbero Sánchez Á. Novel 1,2,4-oxadiazole compounds as PPAR-α ligand agonists: a new strategy for the design of antitumour compounds. RSC Med Chem 2023; 14:1377-1388. [PMID: 37484563 PMCID: PMC10357926 DOI: 10.1039/d3md00063j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/22/2023] [Indexed: 07/25/2023] Open
Abstract
Modulation of PPAR-α by natural ligands is a novel strategy for the development of anticancer therapies. A series of 16 compounds based on the structure of 3-(pyridin-3-yl)-5-(thiophen-3-yl)-1,2,4-oxadiazole (natural compound) with antitumour potential were designed and synthesised. The cytotoxicity and PPAR agonist activity of these synthetic 1,2,4-oxadiazoles were evaluated in the A-498 and DU 145 tumour cell lines. Preliminary biological evaluation showed that most of these synthetic 1,2,4-oxadiazoles are less cytotoxic (sulforhodamine B assay) than the positive control WY-14643. Regarding the PPAR-α modulation, compound 16 was the most active, with EC50 = 0.23-0.83 μM (PPAR-α). Additionally, compound 16 had a similar activity to the natural compound (EC50 = 0.18-0.77 μM) and was less toxic in the RPTEC and WPMY-1 cell lines (non-tumour cells) (CC50 = 81.66-92.67 μM) than the natural compound. Looking at the link between chemical structure and activity, our study demonstrates that changes to the natural 1,2,4-oxadiazole at the level of the thiophenyl residue can lead to new agonists of PPAR-α with promising anti-tumour activity.
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Affiliation(s)
- Luis Apaza Ticona
- Organic Chemistry Unit, Department of Chemistry in Pharmaceutical Sciences, Faculty of Pharmacy, Universidad Complutense of Madrid Plaza Ramón y Cajal s/n 28040 Madrid Spain
- Department of Organic Chemistry, Faculty of Sciences, University Autónoma of Madrid Cantoblanco 28040 Madrid Spain
| | | | | | - Carmen Soriano Vázquez
- Faculty of Pharmacy, Universidad Complutense of Madrid Plaza Ramón y Cajal s/n 28040 Madrid Spain
| | - Carmen Hernán Vieco
- Faculty of Pharmacy, Universidad Complutense of Madrid Plaza Ramón y Cajal s/n 28040 Madrid Spain
| | - Ángel Rumbero Sánchez
- Department of Organic Chemistry, Faculty of Sciences, University Autónoma of Madrid Cantoblanco 28040 Madrid Spain
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23
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Paškevičius T, Lapinskaitė R, Stončius S, Sadzevičienė R, Judžentienė A, Labanauskas L. Palladium-Catalyzed Synthesis of Cyclopropylthiophenes and Their Derivatization. Molecules 2023; 28:molecules28093770. [PMID: 37175178 PMCID: PMC10180236 DOI: 10.3390/molecules28093770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
The cyclopropylthiophene moiety has attracted the attention of the scientific community for its potential pharmaceutical applications. However, synthesis of the compounds containing this framework remains challenging, has rarely been reported and remains unresolved. Here we provide optimized syntheses for cyclopropylthiophenes and their derivatives, containing carbonyl, acetyl, carboxylic acid, methyl carboxylate, nitrile, bromide and sulfonyl chloride moieties.
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Affiliation(s)
- Tomas Paškevičius
- Department of Organic Chemistry, Center for Physical Sciences and Technology (FTMC), Akademijos g. 7, LT-08412 Vilnius, Lithuania
| | - Ringailė Lapinskaitė
- Department of Organic Chemistry, Center for Physical Sciences and Technology (FTMC), Akademijos g. 7, LT-08412 Vilnius, Lithuania
| | - Sigitas Stončius
- Department of Organic Chemistry, Center for Physical Sciences and Technology (FTMC), Akademijos g. 7, LT-08412 Vilnius, Lithuania
| | - Rita Sadzevičienė
- Department of Organic Chemistry, Center for Physical Sciences and Technology (FTMC), Akademijos g. 7, LT-08412 Vilnius, Lithuania
| | - Asta Judžentienė
- Department of Organic Chemistry, Center for Physical Sciences and Technology (FTMC), Akademijos g. 7, LT-08412 Vilnius, Lithuania
| | - Linas Labanauskas
- Department of Organic Chemistry, Center for Physical Sciences and Technology (FTMC), Akademijos g. 7, LT-08412 Vilnius, Lithuania
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24
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Park J, Moon SK, Lee C. N-methylsansalvamide elicits antitumor effects in colon cancer cells in vitro and in vivo by regulating proliferation, apoptosis, and metastatic capacity. Front Pharmacol 2023; 14:1146966. [PMID: 37007044 PMCID: PMC10060634 DOI: 10.3389/fphar.2023.1146966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
N-methylsansalvamide (MSSV), a cyclic pentadepsipeptide, was obtained from a strain of Fusarium solani f. radicicola. The current study investigated the anti-colorectal cancer effect of MSSV. MSSV exhibited the inhibition of the proliferation in HCT116 cells via induction of G0/G1 cell cycle arrest by downregulating CDK 2, CDK6, cyclin D, and cyclin E, and upregulating p21WAF1 and p27KIP1. Decreased phosphorylation of AKT was observed in MSSV-treated cells. Moreover, MSSV treatment induced caspase-mediated apoptosis through elevating the level of cleaved caspase 3, cleaved PARP, cleaved caspase 9, and pro-apoptotic Bax. MSSV revealed the declined MMP-9 level mediated by reduction in the binding activity of AP-1, Sp-1, and NF-κB motifs, which led to the migration and invasion of HCT116 cells. In vitro metabolism with rat liver S9 fractions was performed to examine the effect of MSSV metabolites. The metabolic process enhanced the inhibitory effect of MSSV on the HCT116 cell proliferation via decline of cyclin D1 expression and AKT phosphorylation. Finally, oral administration of MSSV inhibited the tumor growth of HCT116 xenograft mice. These results suggest that MSSV is a potential anti-tumor agent in colorectal cancer treatment.
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Affiliation(s)
- Juhee Park
- Food Analysis Research Center, Food Industry Research Division, Korea Food Research Institute, Wanju, Republic of Korea
- Department of Food Science and Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Sung-Kwon Moon
- Department of Food and Nutrition, Chung-Ang University, Anseong, Republic of Korea
- *Correspondence: Sung-Kwon Moon, ; Chan Lee,
| | - Chan Lee
- Department of Food Science and Biotechnology, Chung-Ang University, Anseong, Republic of Korea
- *Correspondence: Sung-Kwon Moon, ; Chan Lee,
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25
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Metwally HM, Khalaf NA, Abdel-Latif E, Ismail MA. Synthesis, DFT investigations, antioxidant, antibacterial activity and SAR-study of novel thiophene-2-carboxamide derivatives. BMC Chem 2023; 17:6. [PMID: 36803621 PMCID: PMC9940361 DOI: 10.1186/s13065-023-00917-2] [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: 08/23/2022] [Accepted: 02/03/2023] [Indexed: 02/22/2023] Open
Abstract
Synthetic strategy for the synthesis of thiophene 2-carboxamide derivatives substituted with hydroxyl, methyl and amino groups at position-3 was proposed. The strategy includes the cyclization of the precursor ethyl 2-arylazo-3-mercapto-3-(phenylamino)acrylate derivatives, 2-acetyl-2-arylazo-thioacetanilide derivatives and N-aryl-2-cyano-3-mercapto-3-(phenylamino)acrylamide derivatives with N-(4-acetylphenyl)-2-chloroacetamide in alcoholic sodium ethoxide. IR, 1H NMR, and mass spectroscopic analyses were used to characterize the synthesized derivatives. In addition, molecular, electronic properties of the synthesized products were studied by the density functional theory (DFT) where they exhibited close HOMO-LUMO energy gap (ΔEH-L) in which the amino derivatives 7a-c have the highest while the methyl derivatives 5a-c were the lowest. Using the ABTS method, the antioxidant properties of the produced compounds were evaluated, where amino thiophene-2-carboxamide 7a exhibit significant inhibition activity 62.0% compared to ascorbic acid The antibacterial activity against two pathogenic Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis) and two of pathogenic Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) revealed that 7b records the highest activity index compared to ampicillin 83.3, 82.6, 64.0, 86.9%, respectively. Furthermore, the thiophene-2-carboxamide derivatives were docked with five different proteins with the use molecular docking tools and the results explained interactions between amino acid residue of enzyme and compounds. Compounds 3b and 3c showed the highest binding score with 2AS1 protein.
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Affiliation(s)
- Heba M. Metwally
- grid.10251.370000000103426662Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516 Egypt
| | - Norhan A. Khalaf
- grid.10251.370000000103426662Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516 Egypt
| | - Ehab Abdel-Latif
- grid.10251.370000000103426662Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516 Egypt
| | - Mohamed A. Ismail
- grid.10251.370000000103426662Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516 Egypt
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26
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Qin X, Xie C, Hakenjos JM, MacKenzie KR, Boyd SR, Barzi M, Bissig KD, Young DW, Li F. The roles of Cyp1a2 and Cyp2d in pharmacokinetic profiles of serotonin and norepinephrine reuptake inhibitor duloxetine and its metabolites in mice. Eur J Pharm Sci 2023; 181:106358. [PMID: 36513193 PMCID: PMC10395004 DOI: 10.1016/j.ejps.2022.106358] [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: 09/20/2022] [Revised: 11/03/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Duloxetine (DLX) is widely used to treat major depressive disorder. Little is known about the mechanistic basis for DLX-related adverse effects (e.g., liver injury). Human CYP1A2 and CYP2D6 mainly contributes to DLX metabolism, which was proposed to be involved in its adverse effects. Here, we investigated the roles of Cyp1a2 and Cyp2d on DLX pharmacokinetic profile and tissue distribution using a Cyp1a2 knockout (Cyp1a2-KO) mouse model together with a Cyp2d inhibitor (propranolol). Cyp1a2-KO has the few effects on the systematic exposure (area under the plasma concentration-time curve, AUC) and tissue disposition of DLX and its primary metabolites. Propranolol dramatically increased the AUCs of DLX by 3 folds and 1.5 folds in WT and Cyp1a2-KO mice, respectively. Meanwhile, Cyp2d inhibitor decreased the AUC of Cyp2d-involved DLX metabolites (e.g., M16). Mouse tissue distribution revealed that DLX and its major metabolites were the most abundant in kidney, followed by liver and lung with/without Cyp2d inhibitor. Cyp2d inhibitor significantly increased DLX levels in tissues (e.g., liver) in WT and KO mice and decreases the levels of M3, M15, M16 and M17, while it increased the levels of M4, M28 and M29 in tissues. Our findings indicated that Cyp2d play a fundamental role on DLX pharmacokinetic profile and tissue distribution in mice. Clinical studies suggested that CYP1A2 has more effects on DLX systemic exposure than CYP2D6. Further studies in liver humanized mice or clinical studies concerning CYP2D6 inhibitors-DLX interaction study could clarify the roles of CYP2D6 on DLX pharmacokinetics and toxicity in human.
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Affiliation(s)
- Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cen Xie
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - John M Hakenjos
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin R MacKenzie
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA; NMR and Drug Metabolism Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shelton R Boyd
- Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mercedes Barzi
- Department of Pediatrics, Duke University Medical Center, Durham, NC 27708, USA
| | - Karl-Dimiter Bissig
- Department of Pediatrics, Duke University Medical Center, Durham, NC 27708, USA
| | - Damian W Young
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA; NMR and Drug Metabolism Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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Mikhail DS, El-Nassan HB, Mahmoud ST, Fahim SH. Nonacidic thiophene-based derivatives as potential analgesic and design, synthesis, biological evaluation, and metabolic stability study. Drug Dev Res 2022; 83:1739-1757. [PMID: 36074734 DOI: 10.1002/ddr.21992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/23/2022] [Accepted: 08/02/2022] [Indexed: 12/29/2022]
Abstract
Nonsteroidal anti-inflammatory drugs represent one of the most popularly used classes of drugs. However, their long-term administration is associated with various side effects including gastrointestinal ulceration. One of the major reasons of NSAIDs ulcerogenicity is direct damage of the epithelial lining cells by the acidic moieties present in many drugs. Another drawback for this acidic group is its rapid metabolism and clearance through Phase II conjugation. Three series of thiophene and thienopyrimidine derivatives were designed and synthesized as nonacidic anti-inflammatory agents. In vivo testing of their analgesic activity indicated that compounds 2b and 7a-d showed higher PI values than that of the positive control drugs, indomethacin and celecoxib. The latter compounds 2b and 7a-d were subjected to further anti-inflammatory activity testing where they showed comparable percentage edema inhibition to that of indomethacin and celecoxib. Compounds 2b, 7a, 7c, and 7d inhibited PGE2 synthesis by 61.10%-74.54% (71.47% for indomethacin, and 80.11% for celecoxib). The same compounds inhibited the expression of rat mPGES-1 and cPGES3 by 74%-83% (77% for indomethacin, and 82% for celecoxib) and 48%-70% (62% for indomethacin, and 70% for celecoxib), respectively. The stability of the most active compound 2b in Nonenzymatic gastrointestinal fluids and in human plasma was tested. Additionally, studying the metabolic stability of compound 2b in S9 rat liver fraction showed that it displayed a slow in vitro clearance with half-life time 1.5-fold longer than indomethacin. The metabolites of 2b were predicted via UPLC-MS/MS. In silico ADMET profiling study was also included.
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Affiliation(s)
- Demiana S Mikhail
- Department, of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Hala B El-Nassan
- Department, of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Sally T Mahmoud
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Samar H Fahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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Huang Q, Chen Y, Zhang Z, Xue Z, Hua Z, Luo X, Li Y, Lu C, Lu A, Liu Y. The endoplasmic reticulum participated in drug metabolic toxicity. Cell Biol Toxicol 2022; 38:945-961. [PMID: 35040016 DOI: 10.1007/s10565-021-09689-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/07/2021] [Indexed: 01/25/2023]
Abstract
Covalent binding of reactive metabolites formed by drug metabolic activation with biological macromolecules is considered to be an important mechanism of drug metabolic toxicity. Recent studies indicate that the endoplasmic reticulum (ER) could play an important role in drug toxicity by participating in the metabolic activation of drugs and could be a primarily attacked target by reactive metabolites. In this article, we summarize the generation and mechanism of reactive metabolites in ER stress and their associated cell death and inflammatory cascade, as well as the systematic modulation of unfolded protein response (UPR)-mediated adaptive pathways.
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Affiliation(s)
- Qingcai Huang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Youwen Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Zhengjia Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Zeyu Xue
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Zhenglai Hua
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xinyi Luo
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yang Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Cheng Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Aiping Lu
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong, China
| | - Yuanyan Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China.
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29
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Claesson A, Parkes K. Non-innocuous Consequences of Metabolic Oxidation of Alkyls on Arenes. J Med Chem 2022; 65:11433-11453. [PMID: 36001003 DOI: 10.1021/acs.jmedchem.2c00833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactive metabolite (RM) formation is widely accepted as playing a pivotal role in causing adverse idiosyncratic drug reactions, with most attention paid to drug-induced liver injury. Mechanisms of RM formation are determined by the drug's properties in relation to human enzymes transforming the drug. This Perspective focuses on enzymatic oxidation of alkyl groups on aromatics leading to quinone methides and benzylic alcohol sulfates as RMs, a topic that has not received very much attention. Unlike previous overviews, we will include in our Perspective several fulvene-like methides such as 3-methyleneindole. We also speculate that a few older drugs may form non-reported methides of this class. In addition, we report a few guiding DFT calculations of changes in free energy on going from a benzylic alcohol to the corresponding methide. Particularly facile reactions of 2-aminothiazole-5-methanol and 4-aminobenzyl alcohol are noted.
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Affiliation(s)
- Alf Claesson
- Awametox AB, Lilldalsvägen 17 A, SE-14461 Rönninge, Sweden
| | - Kevin Parkes
- Consultant, 39 Cashio Lane, Letchworth Garden City, Hertfordshire SG6 1AY, U.K
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30
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Ring replacement recommender: Ring modifications for improving biological activity. Eur J Med Chem 2022; 238:114483. [DOI: 10.1016/j.ejmech.2022.114483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/19/2022]
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Pagare PP, Li M, Zheng Y, Kulkarni AS, Obeng S, Huang B, Ruiz C, Gillespie JC, Mendez RE, Stevens DL, Poklis JL, Halquist MS, Dewey WL, Selley DE, Zhang Y. Design, Synthesis, and Biological Evaluation of NAP Isosteres: A Switch from Peripheral to Central Nervous System Acting Mu-Opioid Receptor Antagonists. J Med Chem 2022; 65:5095-5112. [PMID: 35255685 PMCID: PMC10149103 DOI: 10.1021/acs.jmedchem.2c00087] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The μ opioid receptor (MOR) has been an intrinsic target to develop treatment of opioid use disorders (OUD). Herein, we report our efforts on developing centrally acting MOR antagonists by structural modifications of 17-cyclopropylmethyl-3,14-dihydroxy-4,5α-epoxy-6β-[(4'-pyridyl) carboxamido] morphinan (NAP), a peripherally acting MOR-selective antagonist. An isosteric replacement concept was applied and incorporated with physiochemical property predictions in the molecular design. Three analogs, namely, 25, 26, and 31, were identified as potent MOR antagonists in vivo with significantly fewer withdrawal symptoms than naloxone observed at similar doses. Furthermore, brain and plasma drug distribution studies supported the outcomes of our design strategy on these compounds. Taken together, our isosteric replacement of pyridine with pyrrole, furan, and thiophene provided insights into the structure-activity relationships of NAP and aided the understanding of physicochemical requirements of potential CNS acting opioids. These efforts resulted in potent, centrally efficacious MOR antagonists that may be pursued as leads to treat OUD.
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Affiliation(s)
- Piyusha P Pagare
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, Virginia 23219, United States
| | - Mengchu Li
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, Virginia 23219, United States
| | - Yi Zheng
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, Virginia 23219, United States
| | - Abhishek S Kulkarni
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, Virginia 23219, United States
| | - Samuel Obeng
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, Virginia 23219, United States
| | - Boshi Huang
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, Virginia 23219, United States
| | - Christian Ruiz
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, Virginia 23219, United States
| | - James C Gillespie
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 410 North 12th Street, Richmond, Virginia 23298, United States
| | - Rolando E Mendez
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 410 North 12th Street, Richmond, Virginia 23298, United States
| | - David L Stevens
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 410 North 12th Street, Richmond, Virginia 23298, United States
| | - Justin L Poklis
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 410 North 12th Street, Richmond, Virginia 23298, United States
| | - Matthew S Halquist
- Department of Pharmaceutics, Virginia Commonwealth University, 410 North 12th Street, Richmond, Virginia 23298, United States
| | - William L Dewey
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 410 North 12th Street, Richmond, Virginia 23298, United States
| | - Dana E Selley
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, 410 North 12th Street, Richmond, Virginia 23298, United States
| | - Yan Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, Virginia 23219, United States
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32
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Small-molecule inhibitors of Slack potassium channels as potential therapeutics for childhood epilepsies. Pharm Pat Anal 2022; 11:45-56. [PMID: 35369761 PMCID: PMC9260495 DOI: 10.4155/ppa-2022-0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Slack channels are sodium-activated potassium channels that are encoded by the KCNT1 gene. Several KCNT1 gain of function mutations have been linked to malignant migrating partial seizures of infancy. Quinidine is an anti-arrhythmic drug that functions as a moderately potent inhibitor of Slack channels; however, quinidine use is limited by its poor selectivity, safety and pharmacokinetic profile. Slack channels represent an interesting target for developing novel therapeutics for the treatment of malignant migrating partial seizures of infancy and other childhood epilepsies; thus, ongoing efforts are directed toward the discovery of small-molecules that inhibit Slack currents. This review summarizes patent applications published in 2020-2021 that describe the discovery of novel small-molecule Slack inhibitors.
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33
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Borah B, Dwivedi KD, Kumar B, Chowhan LR. Recent advances in the microwave- and ultrasound-assisted green synthesis of coumarin-heterocycles. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2021.103654] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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34
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Prigaro BJ, Esquer H, Zhou Q, Pike LA, Awolade P, Lai XH, Abraham AD, Abbott JM, Matter B, Kompella UB, Messersmith WA, Gustafson DL, LaBarbera DV. Design, Synthesis, and Biological Evaluation of the First Inhibitors of Oncogenic CHD1L. J Med Chem 2022; 65:3943-3961. [PMID: 35192363 DOI: 10.1021/acs.jmedchem.1c01778] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chromodomain helicase DNA-binding protein 1 like (CHD1L) is an oncogene implicated in tumor progression, multidrug resistance, and metastasis in many types of cancer. In this article, we described the optimization of the first lead CHD1L inhibitors (CHD1Li) through drug design and medicinal chemistry. More than 30 CHD1Li were synthesized and evaluated using a variety of colorectal cancer (CRC) tumor organoid models and functional assays. The results led to the prioritization of six lead CHD1Li analogues with improved potency, antitumor activity, and drug-like properties including metabolic stability and in vivo pharmacokinetics. Furthermore, lead CHD1Li 6.11 proved to be an orally bioavailable antitumor agent, significantly reducing the tumor volume of CRC xenografts generated from isolated quasi mesenchymal cells (M-phenotype), which possess enhanced tumorigenic properties. In conclusion, we reported the optimization of first-in-class inhibitors of oncogenic CHD1L as a novel therapeutic strategy with potential for the treatment of cancer.
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Affiliation(s)
- Brett J Prigaro
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, The CU Cancer Center, Aurora, Colorado 80045, United States
| | - Hector Esquer
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, The CU Cancer Center, Aurora, Colorado 80045, United States
| | - Qiong Zhou
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, The CU Cancer Center, Aurora, Colorado 80045, United States
| | - Laura A Pike
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, The CU Cancer Center, Aurora, Colorado 80045, United States
| | - Paul Awolade
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, The CU Cancer Center, Aurora, Colorado 80045, United States
| | - Xin-He Lai
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, The CU Cancer Center, Aurora, Colorado 80045, United States
| | - Adedoyin D Abraham
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, The CU Cancer Center, Aurora, Colorado 80045, United States
| | - Joshua M Abbott
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, The CU Cancer Center, Aurora, Colorado 80045, United States
| | - Brock Matter
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, The CU Cancer Center, Aurora, Colorado 80045, United States
| | - Uday B Kompella
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, The CU Cancer Center, Aurora, Colorado 80045, United States.,The University of Colorado (CU) Anschutz Medical Campus (AMC) Center for Drug Discovery, The CU Cancer Center, Aurora, Colorado 80045, United States
| | - Wells A Messersmith
- The School of Medicine, Division of Medical Oncology, The CU Cancer Center, Aurora, Colorado 80045, United States.,The University of Colorado (CU) Anschutz Medical Campus (AMC) Center for Drug Discovery, The CU Cancer Center, Aurora, Colorado 80045, United States.,The CU Cancer Center, Aurora, Colorado 80045, United States
| | - Daniel L Gustafson
- Flint Animal Cancer Center and Department of Clinical Sciences, School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado 80523, United States.,The University of Colorado (CU) Anschutz Medical Campus (AMC) Center for Drug Discovery, The CU Cancer Center, Aurora, Colorado 80045, United States.,The CU Cancer Center, Aurora, Colorado 80045, United States
| | - Daniel V LaBarbera
- The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, The CU Cancer Center, Aurora, Colorado 80045, United States.,The University of Colorado (CU) Anschutz Medical Campus (AMC) Center for Drug Discovery, The CU Cancer Center, Aurora, Colorado 80045, United States.,The CU Cancer Center, Aurora, Colorado 80045, United States
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35
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Ibrahim SRM, Omar AM, Bagalagel AA, Diri RM, Noor AO, Almasri DM, Mohamed SGA, Mohamed GA. Thiophenes-Naturally Occurring Plant Metabolites: Biological Activities and In Silico Evaluation of Their Potential as Cathepsin D Inhibitors. PLANTS (BASEL, SWITZERLAND) 2022; 11:539. [PMID: 35214871 PMCID: PMC8877444 DOI: 10.3390/plants11040539] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/03/2022] [Accepted: 02/12/2022] [Indexed: 05/03/2023]
Abstract
Naturally, thiophenes represent a small family of natural metabolites featured by one to five thiophene rings. Numerous plant species belonging to the family Asteraceae commonly produce thiophenes. These metabolites possessed remarkable bioactivities, including antimicrobial, antiviral, anti-inflammatory, larvicidal, antioxidant, insecticidal, cytotoxic, and nematicidal properties. The current review provides an update over the past seven years for the reported natural thiophene derivatives, including their sources, biosynthesis, spectral data, and bioactivities since the last review published in 2015. Additionally, with the help of the SuperPred webserver, an AI (artificial intelligence) tool, the potential drug target for the compounds was predicted. In silico studies were conducted for Cathepsin D with thiophene derivatives, including ADMET (drug absorption/distribution/metabolism/excretion/and toxicity) properties prediction, molecular docking for the binding interaction, and molecular dynamics to evaluate the ligand-target interaction stability under simulated physiological conditions.
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Affiliation(s)
- Sabrin R. M. Ibrahim
- Department of Chemistry, Preparatory Year Program, Batterjee Medical College, Jeddah 21442, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Abdelsattar M. Omar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Alaa A. Bagalagel
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.A.B.); (R.M.D.); (A.O.N.); (D.M.A.)
| | - Reem M. Diri
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.A.B.); (R.M.D.); (A.O.N.); (D.M.A.)
| | - Ahmad O. Noor
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.A.B.); (R.M.D.); (A.O.N.); (D.M.A.)
| | - Diena M. Almasri
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.A.B.); (R.M.D.); (A.O.N.); (D.M.A.)
| | | | - Gamal A. Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
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36
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Molecular modeling and antioxidant activity of newly synthesized 3‑hydroxy-2-substituted-thiophene derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Monooxygenase- and Dioxygenase-Catalyzed Oxidative Dearomatization of Thiophenes by Sulfoxidation, cis-Dihydroxylation and Epoxidation. Int J Mol Sci 2022; 23:ijms23020909. [PMID: 35055091 PMCID: PMC8777831 DOI: 10.3390/ijms23020909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 11/17/2022] Open
Abstract
Enzymatic oxidations of thiophenes, including thiophene-containing drugs, are important for biodesulfurization of crude oil and drug metabolism of mono- and poly-cyclic thiophenes. Thiophene oxidative dearomatization pathways involve reactive metabolites, whose detection is important in the pharmaceutical industry, and are catalyzed by monooxygenase (sulfoxidation, epoxidation) and dioxygenase (sulfoxidation, dihydroxylation) enzymes. Sulfoxide and epoxide metabolites of thiophene substrates are often unstable, and, while cis-dihydrodiol metabolites are more stable, significant challenges are presented by both types of metabolite. Prediction of the structure, relative and absolute configuration, and enantiopurity of chiral metabolites obtained from thiophene enzymatic oxidation depends on the substrate, type of oxygenase selected, and molecular docking results. The racemization and dimerization of sulfoxides, cis/trans epimerization of dihydrodiol metabolites, and aromatization of epoxides are all factors associated with the mono- and di-oxygenase-catalyzed metabolism of thiophenes and thiophene-containing drugs and their applications in chemoenzymatic synthesis and medicine.
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38
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Santiago C, Jiménez-Aberasturi X, Leicea E, Lete MG, Sotomayor N, Lete E. Microwave-assisted palladium catalysed C-H acylation with aldehydes: synthesis and diversification of 3-acylthiophenes. Org Biomol Chem 2022; 20:852-861. [PMID: 35001098 DOI: 10.1039/d1ob02176a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of MW allows the efficient palladium(II)-catalysed C-3 acylation of thiophenes with aldehydes via C(sp2)-H activation for the synthesis of (cyclo)alkyl/aryl thienyl ketones (43 examples). Compared to standard thermal conditions, the use of MW reduces the reaction time (15 to 30 min vs. 1 to 3 hours), leading to improved yields of the ketones (up to 92%). The control of positional selectivity is achieved by 2-pyridinyl and 2-pyrimidyl ortho-directing groups at C-2 of the thiophene scaffold. To show the synthetic applicability, selected ketones were subjected to further transformations, including intramolecular reactions to directly embed the directing group in the core structure of the new molecule.
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Affiliation(s)
- Carlos Santiago
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain.
| | - Xabier Jiménez-Aberasturi
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain.
| | - Eztizen Leicea
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain.
| | - Marta G Lete
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, Derio 48170, Spain
| | - Nuria Sotomayor
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain.
| | - Esther Lete
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain.
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Rampon D, Seckler D, da Luz EQ, Paixão DB, Larroza AME, Schneider PH, Alves D. Transition metal catalysed direct sulfanylation of unreactive C-H bonds: an overview of the last two decades. Org Biomol Chem 2022; 20:6072-6177. [DOI: 10.1039/d2ob00986b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transition metal catalysed direct sulfanylations of unreactive C-H bonds have become a unique and straightforward synthetic strategy in late-stage C-S bond formation of relevant complex molecules. Such transformations have represented...
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Paixão DB, Soares EGO, Salles HD, Silva CDG, Rampon DS, Schneider PH. Rongalite in PEG-400 as a general and reusable system for the synthesis of 2,5-disubstituted chalcogenophenes. Org Chem Front 2022. [DOI: 10.1039/d2qo01069k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Herein we report the use of rongalite in PEG-400 as a general, efficient, and environmentally benign reductive system for the synthesis of a wide range of 2,5-disubstituted chalcogenophenes from elemental sulfur, selenium and tellurium.
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Affiliation(s)
- Douglas B. Paixão
- Instituto de Química, Departamento de Química Orgânica, Universidade Federal do Rio Grande do Sul (UFRGS), P.O. Box 15003, 91501-970, Porto Alegre, RS, Brazil
| | - Eduardo G. O. Soares
- Instituto de Química, Departamento de Química Orgânica, Universidade Federal do Rio Grande do Sul (UFRGS), P.O. Box 15003, 91501-970, Porto Alegre, RS, Brazil
| | - Helena D. Salles
- Instituto de Química, Departamento de Química Orgânica, Universidade Federal do Rio Grande do Sul (UFRGS), P.O. Box 15003, 91501-970, Porto Alegre, RS, Brazil
| | - Caren D. G. Silva
- Instituto de Química, Departamento de Química Orgânica, Universidade Federal do Rio Grande do Sul (UFRGS), P.O. Box 15003, 91501-970, Porto Alegre, RS, Brazil
| | - Daniel S. Rampon
- Laboratório de Polímeros e Catálise (LAPOCA), Departamento de Química, Universidade Federal do Paraná (UFPR), P.O. Box 19061, 81531-990, Curitiba, PR, Brazil
| | - Paulo H. Schneider
- Instituto de Química, Departamento de Química Orgânica, Universidade Federal do Rio Grande do Sul (UFRGS), P.O. Box 15003, 91501-970, Porto Alegre, RS, Brazil
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Lagardère P, Fersing C, Masurier N, Lisowski V. Thienopyrimidine: A Promising Scaffold to Access Anti-Infective Agents. Pharmaceuticals (Basel) 2021; 15:35. [PMID: 35056092 PMCID: PMC8780093 DOI: 10.3390/ph15010035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022] Open
Abstract
Thienopyrimidines are widely represented in the literature, mainly due to their structural relationship with purine base such as adenine and guanine. This current review presents three isomers-thieno[2,3-d]pyrimidines, thieno[3,2-d]pyrimidines and thieno[3,4-d]pyrimidines-and their anti-infective properties. Broad-spectrum thienopyrimidines with biological properties such as antibacterial, antifungal, antiparasitic and antiviral inspired us to analyze and compile their structure-activity relationship (SAR) and classify their synthetic pathways. This review explains the main access route to synthesize thienopyrimidines from thiophene derivatives or from pyrimidine analogs. In addition, SAR study and promising anti-infective activity of these scaffolds are summarized in figures and explanatory diagrams. Ligand-receptor interactions were modeled when the biological target was identified and the crystal structure was solved.
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Affiliation(s)
- Prisca Lagardère
- IBMM, University of Montpellier, CNRS, ENSCM, 34293 Montpellier, France; (P.L.); (C.F.); (V.L.)
| | - Cyril Fersing
- IBMM, University of Montpellier, CNRS, ENSCM, 34293 Montpellier, France; (P.L.); (C.F.); (V.L.)
- Nuclear Medicine Department, Montpellier Cancer Institute (ICM), University of Montpellier, 208 Avenue des Apothicaires, CEDEX 5, 34298 Montpellier, France
| | - Nicolas Masurier
- IBMM, University of Montpellier, CNRS, ENSCM, 34293 Montpellier, France; (P.L.); (C.F.); (V.L.)
| | - Vincent Lisowski
- IBMM, University of Montpellier, CNRS, ENSCM, 34293 Montpellier, France; (P.L.); (C.F.); (V.L.)
- Department of Pharmacy, Lapeyronie Hospital, CHU Montpellier, 191 Av. du Doyen Gaston Giraud, 34295 Montpellier, France
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Wang T, Zhu X, Tao Q, Xu W, Sun H, Wu P, Cheng B, Zhai H. Synthesis of tetrasubstituted thiophenes from pyridinium 1,4-zwitterionic thiolates and modified activated alkynes. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Douroudgari H, Vahedpour M. A computer-aided method for controlling chemical resistance of drugs using RRKM theory in the liquid phase. Sci Rep 2021; 11:22971. [PMID: 34836999 PMCID: PMC8626518 DOI: 10.1038/s41598-021-01751-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/02/2021] [Indexed: 12/03/2022] Open
Abstract
The chemical resistance of drugs against any change in their composition and studying the rate of multiwell-multichannel reactions in the liquid phase, respectively, are the important challenges of pharmacology and chemistry. In this article, we investigate two challenges together through studying drug stability against its unimolecular reactions in the liquid phase. Accordingly, multiwell-multichannel reactions based on 1,4-H shifts are designed for simplified drugs such as 3-hydroxyl-1H-pyrrol-2(5H)-one, 3-hydroxyfuran-2(5H)-one, and 3-hydroxythiophen-2(5H)-one. After that, the reverse and forward rate constants are calculated by using the Rice Ramsperger Kassel Marcus theory (RRKM) and Eckart tunneling correction over the 298-360 K temperature range. Eventually, using the obtained rate constants, we can judge drug resistance versus structural changes. To attain the goals, the potential energy surfaces of all reactions are computed by the complete basis set-quadratic Becke3 composite method, CBS-QB3, and the high-performance meta hybrid density functional method, M06-2X, along with the universal Solvation Model based on solute electron Density, SMD, due to providing more precise and efficient results for the barrier heights and thermodynamic studies. To find the main reaction pathway of the intramolecular 1,4-H shifts in the target molecules, all possible reaction pathways are considered mechanistically in the liquid phase. Also, the direct dynamics calculations that carry out by RRKM theory on the modeled pathways are used to distinguish the main reaction pathway. As the main finding of this research, the results of quantum chemical calculations accompanied by the RRKM/Eckart rate constants are used to predict the stability of drugs. This study proposes a new way to examine drug stability by the computer-aided reaction design of target drugs. Our results show that 3-hydroxyfuran-2(5H)-one based drugs are the most stable and 3-hydroxythiophen-2(5H)-one based drugs are more stable than 3-hydroxy-1H-pyrrol-2 (5H)-one based drugs in water solution.
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Affiliation(s)
- Hamed Douroudgari
- Department of Chemistry, University of Zanjan, PO Box 38791-45371, Zanjan, Iran.
| | - Morteza Vahedpour
- Department of Chemistry, University of Zanjan, PO Box 38791-45371, Zanjan, Iran.
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Krake EF, Baumann W. Selective Oxidation of Clopidogrel by Peroxymonosulfate (PMS) and Sodium Halide (NaX) System: An NMR Study. Molecules 2021; 26:5921. [PMID: 34641465 PMCID: PMC8512727 DOI: 10.3390/molecules26195921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 11/17/2022] Open
Abstract
A selective transformation of clopidogrel hydrogen sulfate (CLP) by reactive halogen species (HOX) generated from peroxymonosulfate (PMS) and sodium halide (NaX) is described. Other sustainable oxidants as well as different solvents have also been investigated. As result of this study, for each sodium salt the reaction conditions were optimized, and four different degradation products were formed. Three products were halogenated at C-2 on the thiophene ring and have concomitant functional transformation, such as N-oxide in the piperidine group. A halogenated endo-iminium product was also observed. With this condition, a fast preparation of known endo-iminium clopidogrel impurity (new counterion) was reported as well. The progress of the reaction was monitored using nuclear magnetic resonance spectroscopy as an analytical tool and all the products were characterized by 1D-, 2D-NMR and HRMS.
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Affiliation(s)
| | - Wolfgang Baumann
- Leibniz-Institut für Katalyse e.V., Albert-Einstein-Straße 29a, 18059 Rostock, Germany;
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Camilleri P, Soldo B, Buch A, Janusz J. Oxidative metabolism of razuprotafib (AKB-9778), a sulfamic acid phosphatase inhibitor, in human microsomes and recombinant human CYP2C8 enzyme. Xenobiotica 2021; 51:1110-1121. [PMID: 34477046 DOI: 10.1080/00498254.2021.1969482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Razuprotafib, a sulphamic acid-containing phosphatase inhibitor, is shown in vivo to undergo enzymatic oxidation and methylation to form a major metabolite in monkey and human excreta with an m/z- value of 633.LC-MS/MS analysis of samples derived from incubations of razuprotafib with human liver microsomes and recombinant CYP2C8 enzyme has elucidated the metabolic pathway for formation of the thiol precursor to the S-methyl metabolite MS633 (m/z- 633).Under in vitro conditions, the major pathway of razuprotafib metabolism involves extensive oxidation of the thiophene and phenyl rings.A single oxidation takes place at one of the phenyl groups. Multiple oxidations occur at the thiophene moiety: initial oxidation results in the formation of a thiolactone followed by a second oxidation giving rise to an S-oxide of the thiolactone, which is further metabolised to the ring-opened form and ultimate formation of a thiol (m/z- 619).An additional mono-oxidation pathway involves epoxidation of the thiophene followed by hydrolysis to a diol.The thiol and diol metabolites are trapped by the addition of a nucleophilic trapping agent, 3-methoxyphenacyl bromide (MPB), giving adducts with m/z- 767.The thiol is a likely precursor to the major in vivo razuprotafib metabolite, MS633.
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Draper-Joyce CJ, Bhola R, Wang J, Bhattarai A, Nguyen ATN, Cowie-Kent I, O'Sullivan K, Chia LY, Venugopal H, Valant C, Thal DM, Wootten D, Panel N, Carlsson J, Christie MJ, White PJ, Scammells P, May LT, Sexton PM, Danev R, Miao Y, Glukhova A, Imlach WL, Christopoulos A. Positive allosteric mechanisms of adenosine A 1 receptor-mediated analgesia. Nature 2021; 597:571-576. [PMID: 34497422 PMCID: PMC8711093 DOI: 10.1038/s41586-021-03897-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
The adenosine A1 receptor (A1R) is a promising therapeutic target for non-opioid analgesic agents to treat neuropathic pain1,2. However, development of analgesic orthosteric A1R agonists has failed because of a lack of sufficient on-target selectivity as well as off-tissue adverse effects3. Here we show that [2-amino-4-(3,5-bis(trifluoromethyl)phenyl)thiophen-3-yl)(4-chlorophenyl)methanone] (MIPS521), a positive allosteric modulator of the A1R, exhibits analgesic efficacy in rats in vivo through modulation of the increased levels of endogenous adenosine that occur in the spinal cord of rats with neuropathic pain. We also report the structure of the A1R co-bound to adenosine, MIPS521 and a Gi2 heterotrimer, revealing an extrahelical lipid-detergent-facing allosteric binding pocket that involves transmembrane helixes 1, 6 and 7. Molecular dynamics simulations and ligand kinetic binding experiments support a mechanism whereby MIPS521 stabilizes the adenosine-receptor-G protein complex. This study provides proof of concept for structure-based allosteric drug design of non-opioid analgesic agents that are specific to disease contexts.
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Affiliation(s)
- Christopher J Draper-Joyce
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Rebecca Bhola
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Anh T N Nguyen
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - India Cowie-Kent
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kelly O'Sullivan
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ling Yeong Chia
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Hariprasad Venugopal
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Celine Valant
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - David M Thal
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Denise Wootten
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Nicolas Panel
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Macdonald J Christie
- Discipline of Pharmacology, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Paul J White
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Peter Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Lauren T May
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Patrick M Sexton
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Alisa Glukhova
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
- Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Victoria, Australia.
| | - Wendy L Imlach
- Department of Physiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Arthur Christopoulos
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
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Alhaddad M, Zaki ZI, Amin MS. Application of SrRuO3 Nanoparticles Supported with Reduced Graphene Oxide for Degradation of Thiophene Under Visible Light Irradiation. J Inorg Organomet Polym Mater 2021. [DOI: 10.1007/s10904-021-01969-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Sol–Gel Assembled Ag3VO4/rGO Nanocomposite Photocatalyst for Improved Visible-Light-Photooxidative Desulfurization of Thiophene. J Inorg Organomet Polym Mater 2021. [DOI: 10.1007/s10904-021-01895-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Chikowe I, Phiri AC, Mbewe KP, Matekenya D. In-silico evaluation of Malawi essential medicines and reactive metabolites for potential drug-induced toxicities. BMC Pharmacol Toxicol 2021; 22:36. [PMID: 34134770 PMCID: PMC8207713 DOI: 10.1186/s40360-021-00499-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Drug-induced toxicity is one of the problems that have negatively impacted on the well-being of populations throughout the world, including Malawi. It results in unnecessary hospitalizations, retarding the development of the country. This study assessed the Malawi Essential Medicines List (MEML) for structural alerts and reactive metabolites with the potential for drug-induced toxicities. METHODS This in-silico screening study used StopTox, ToxAlerts and LD-50 values toxicity models to assess the MEML drugs. A total of 296 drugs qualified for the analysis (those that had defined chemical structures) and were screened in each software programme. Each model had its own toxicity endpoints and the models were compared for consensus of their results. RESULTS In the StopTox model, 86% of the drugs had potential to cause at least one toxicity including 55% that had the potential of causing eye irritation and corrosion. In ToxAlerts, 90% of the drugs had the potential of causing at least one toxicity and 72% were found to be potentially reactive, unstable and toxic. In LD-50, 70% of the drugs were potentially toxic. Model consensus evaluation results showed that the highest consensus was observed between ToxAlerts and StopTox (80%). The overall consensus amongst the three models was 57% and statistically significant (p < 0.05). CONCLUSIONS A large number of drugs had the potential to cause various systemic toxicities. But the results need to be interpreted cautiously since the clinical translation of QSAR-based predictions depends on many factors. In addition, inconsistencies have been reported between screening results amongst different models.
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Affiliation(s)
- Ibrahim Chikowe
- Pharmacy Department, College of Medicine, University of Malawi, Blantyre, Malawi.
| | | | - Kirios Patrick Mbewe
- Pharmacy Department, College of Medicine, University of Malawi, Blantyre, Malawi
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Kanova N, Dundar BA, Kelgokmen Y, Zora M. One-Pot Synthesis of 2-Acetyl-1 H-pyrroles from N-Propargylic β-Enaminones via Intermediacy of 1,4-Oxazepines. J Org Chem 2021; 86:6289-6304. [PMID: 33872009 DOI: 10.1021/acs.joc.1c00077] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A one-pot two-step protocol for the synthesis of 2-acetyl-1H-pyrroles from N-propargylic β-enaminones was described. When treated with zinc chloride in refluxing chloroform, N-propargylic β-enaminones produced in situ 2-methylene-2,3-dihydro-1,4-oxazepines, which, upon further refluxing in methanol with zinc chloride, afforded 2-acetyl-1H-pyrroles. The process was found to be general for a wide variety of N-propargylic β-enaminones and yielded a diverse range of 2-acetyl-1H-pyrroles in good to high yields with large substrate scope and good functional group tolerance. This operationally easy method may provide a rapid access to functionalized 2-acetyl-1H-pyrroles of pharmacological interest.
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Affiliation(s)
- Nilay Kanova
- Department of Chemistry, Middle East Technical University, 06800 Ankara, Turkey
| | - Buse Aysen Dundar
- Department of Chemistry, Middle East Technical University, 06800 Ankara, Turkey
| | - Yilmaz Kelgokmen
- Department of Chemistry, Middle East Technical University, 06800 Ankara, Turkey
| | - Metin Zora
- Department of Chemistry, Middle East Technical University, 06800 Ankara, Turkey
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