1
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Ren L, Moreno D, Baer BR, Barbour P, Bettendorf T, Bouhana K, Brown K, Brown SA, Fell JB, Hartley DP, Hicken EJ, Laird ER, Lee P, McCown J, Otten JN, Prigaro B, Wallace R, Kahn D. Identification of the Clinical Candidate PF-07284890 ( ARRY-461), a Highly Potent and Brain Penetrant BRAF Inhibitor for the Treatment of Cancer. J Med Chem 2024. [PMID: 39077892 DOI: 10.1021/acs.jmedchem.4c00998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Mutant BRAFV600E is one of the most common oncogenic drivers in metastatic melanoma. While first generation BRAFV600E inhibitors are capable of controlling tumors systemically, they are unable to adequately treat tumors that have metastasized to the brain due to insufficient penetration across the blood-brain barrier (BBB). Through a combination of structure-based drug design (SBDD) and the optimization of physiochemical properties to enhance BBB penetration, we herein report the discovery of the brain-penetrant BRAFV600E inhibitor PF-07284890 (ARRY-461). In mice studies, ARRY-461 proved to be highly brain-penetrant and was able to drive regressions of A375 BRAFV600E tumors implanted both subcutaneously and intracranially. Based on compelling preclinical safety and efficacy studies, ARRY-461 was progressed into a Phase 1 A/B clinical trial (NCT04543188).
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Affiliation(s)
- Li Ren
- Enliven Therapeutics, Boulder, Colorado 80301, United States
| | - David Moreno
- Enliven Therapeutics, Boulder, Colorado 80301, United States
| | - Brian R Baer
- Pfizer Boulder R&D, Boulder, Colorado 80301, United States
| | | | | | - Karyn Bouhana
- Cogent Biosciences, Boulder, Colorado 80301, United States
| | - Karin Brown
- Pfizer Boulder R&D, Boulder, Colorado 80301, United States
| | - Suzy A Brown
- Pfizer Boulder R&D, Boulder, Colorado 80301, United States
| | - Jay B Fell
- Cogent Biosciences, Boulder, Colorado 80301, United States
| | | | - Erik J Hicken
- Pfizer Boulder R&D, Boulder, Colorado 80301, United States
| | - Ellen R Laird
- Pfizer Boulder R&D, Boulder, Colorado 80301, United States
| | - Patrice Lee
- Pfizer Boulder R&D, Boulder, Colorado 80301, United States
| | - Joseph McCown
- Pfizer Boulder R&D, Boulder, Colorado 80301, United States
| | | | | | - Ross Wallace
- Loxo Oncology, Louisville, Colorado 80027, United States
| | - Dean Kahn
- Pfizer Boulder R&D, Boulder, Colorado 80301, United States
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2
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Chiodi D, Ishihara Y. The role of the methoxy group in approved drugs. Eur J Med Chem 2024; 273:116364. [PMID: 38781921 DOI: 10.1016/j.ejmech.2024.116364] [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: 01/04/2024] [Revised: 03/12/2024] [Accepted: 03/23/2024] [Indexed: 05/25/2024]
Abstract
The methoxy substituent is prevalent in natural products and, consequently, is present in many natural product-derived drugs. It has also been installed in modern drug molecules with no remnant of natural product features because medicinal chemists have been taking advantage of the benefits that this small functional group can bestow on ligand-target binding, physicochemical properties, and ADME parameters. Herein, over 230 methoxy-containing small-molecule drugs, as well as several fluoromethoxy-containing drugs, are presented from the vantage point of the methoxy group. Biochemical mechanisms of action, medicinal chemistry SAR studies, and numerous X-ray cocrystal structures are analyzed to identify the precise role of the methoxy group for many of the drugs and drug classes. Although the methoxy substituent can be considered as the hybridization of a hydroxy and a methyl group, the combination of these functionalities often results in unique effects that can amount to more than the sum of the individual parts.
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Affiliation(s)
- Debora Chiodi
- Department of Chemistry, Takeda Pharmaceuticals, 9625 Towne Centre Drive, San Diego, CA, 92121, USA
| | - Yoshihiro Ishihara
- Department of Chemistry, Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA, 92121, USA.
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3
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Duan M, Qiu C, Huang X, Sun L, He X, Wang Z, Yue H, Wang K, Qi Y, Peng S, Shi X, Xi Z, Tong M, Ding X, Hou Y, Zhao Y. Novel biaryloxazolidinone derivatives with broad-spectrum antibacterial activity, favorable drug-like profiles and in vivo efficacy against linezolid-resistant Staphylococcusaureus. Eur J Med Chem 2024; 273:116493. [PMID: 38761790 DOI: 10.1016/j.ejmech.2024.116493] [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: 04/12/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 05/20/2024]
Abstract
The emergence of multidrug-resistant bacteria along with a declining pipeline of clinically useful antibiotics has led to the urgent need for the development of more effective antibacterial agents to treat drug-resistant bacteria. We previously discovered compound OB-158 with potent antibacterial activity but exhibited poor oral bioavailability. Herein, a systematic structural optimization of OB-158 to improve pharmacokinetic profiles yielded 26 novel biaryloxazolidinone analogues, and their activities against Gram-positive S. aureus, multidrug resistant S. aureus and Enterococcus faecalis were evaluated. Remarkably, compound 8b was identified with potent antibacterial activity against S. aureus (MIC = 0.06 μg/mL), MSSA (MIC = 0.125 μg/mL), MRSA (MIC = 0.06 μg/mL), LRSA (MIC = 0.125 μg/mL) and LREFa (MIC = 0.5 μg/mL). Compound 8b was demonstrated as a promising candidate through druglikeness evaluation including metabolism in microsomes and plasma, Caco-2 cell permeability, plasma protein binding, cytotoxicity, and inhibition of CYP450 and human monoamine oxidase. Notably, compound 8b displayed excellent PK profile with appropriate T1/2 of 1.49 h, high peak plasma concentration (Cmax = 2320 ng/mL), high plasma exposure (AUC0-t = 8310 h ng/mL), and superior oral bioavailability (F = 68.1 %) in Sprague-Dawley rats. Ultimately, in vivo efficacy of compound 8b in a mouse model of LRSA systemic infection was also demonstrated. Taken together, compound 8b represents a promising drug candidate for the treatment of linezolid-resistant Gram-positive bacterial strains infection.
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Affiliation(s)
- Meibo Duan
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Chuang Qiu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Xinyu Huang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Lei Sun
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Xinzi He
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Zechen Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Hao Yue
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Kun Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Yinliang Qi
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Shan Peng
- 3D BioOptima, 1338 Wuzhong Avenue, Suzhou, 215104, China
| | - Xuan Shi
- 3D BioOptima, 1338 Wuzhong Avenue, Suzhou, 215104, China
| | - Zhiguo Xi
- 3D BioOptima, 1338 Wuzhong Avenue, Suzhou, 215104, China
| | - Minghui Tong
- 3D BioOptima, 1338 Wuzhong Avenue, Suzhou, 215104, China
| | - Xiudong Ding
- Department of Clinical Laboratory, The 309th Hospital of Chinese People's Liberation Army, Beijing 100091, China
| | - Yunlei Hou
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China.
| | - Yanfang Zhao
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China.
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4
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Conrad J, Paras NA, Vaz RJ. Model of P-Glycoprotein Ligand Binding and Validation with Efflux Substrate Matched Pairs. J Med Chem 2024; 67:5854-5865. [PMID: 38544305 PMCID: PMC11017244 DOI: 10.1021/acs.jmedchem.4c00139] [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: 01/16/2024] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The blood-brain barrier (BBB) poses a significant obstacle in developing therapeutics for neurodegenerative diseases and central nervous system (CNS) disorders. P-glycoprotein (P-gp), a multidrug resistance protein, is a critical gatekeeper in the BBB and plays a role in cancer chemoresistance. This paper uses cryo-EM P-gp structures as starting points with an induced fit docking (IFD) model to evaluate 19 pairs of compounds with known P-gp efflux data. The study reveals significant differences in binding energy and sheds light on structural modifications' impact on efflux properties. In the cases examined, fluorine incorporation influences the efflux by altering the molecular conformation rather than proximal heteroatom basicity. Although there are limitations in addressing covalent interactions or when binding extends into the more flexible vestibule region of the protein, the results provide valuable insights and potential strategies to overcome P-gp efflux, contributing to the advancement of drug development for both CNS disorders and cancer therapies.
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Affiliation(s)
- Jay Conrad
- Institute
for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Nick A. Paras
- Institute
for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Roy J. Vaz
- Institute
for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158, United States
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5
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Kapre S, Palakurthi SS, Jain A, Palakurthi S. DES-igning the future of drug delivery: A journey from fundamentals to drug delivery applications. J Mol Liq 2024; 400:124517. [DOI: 10.1016/j.molliq.2024.124517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
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6
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Segura-Quezada LA, Hernández-Velázquez ED, Corrales-Escobosa AR, de León-Solis C, Solorio-Alvarado CR. Ningalins, Pyrrole-Bearing Metabolites Isolated from Didemnum spp. Synthesis and MDR-Reversion Activity in Cancer Therapy. Chem Biodivers 2024; 21:e202300883. [PMID: 38010267 DOI: 10.1002/cbdv.202300883] [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: 06/15/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Multi-Drug Resistance (MDR) is one of the most frequent problems observed in the course of cancer chemotherapy. Cells under treatment, tend to develop survival mechanisms to drug-action thus generating drug-resistance. One of the most important mechanism to get it is the over expression of P-gp glycoprotein, which acts as an efflux-pump releasing the drug outside of the cancer cell. A strategy for a succesfull treatment consists in the co-administration of one compound that acts against P-gp and another which acts against the cell during chemotherapy. Ningalins are pyrrole-containing naturally occurring compounds isolated mainly from the marine tunicate Didemnum spp and also they are some of the top reversing agents in MDR treatment acting on P-gp. Considering the relevance displayed for some of these isolated alkaloids or their core as a drug for co-administration in cancer therapy, all the total synthesis described to date for the members of ningalins family are reviewed herein.
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Affiliation(s)
- Luis A Segura-Quezada
- Universidad de Guanajuato, Departamento de Química, División de Ciencias Naturales y Exactas, Campus Guanajuato., Noria Alta S/N, 36050, Guanajuato, Gto., México
| | - Edson D Hernández-Velázquez
- Universidad de Guanajuato, Departamento de Química, División de Ciencias Naturales y Exactas, Campus Guanajuato., Noria Alta S/N, 36050, Guanajuato, Gto., México
| | - Alma R Corrales-Escobosa
- Universidad de Guanajuato, Departamento de Química, División de Ciencias Naturales y Exactas, Campus Guanajuato., Noria Alta S/N, 36050, Guanajuato, Gto., México
| | - Claudia de León-Solis
- Instituto de Investigaciones Químicas, Biológicas, Biomédicas y Biofísicas., Universidad Mariano Gálvez, Guatemala, Guatemala
| | - César R Solorio-Alvarado
- Universidad de Guanajuato, Departamento de Química, División de Ciencias Naturales y Exactas, Campus Guanajuato., Noria Alta S/N, 36050, Guanajuato, Gto., México
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7
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Bonifazi A, Saab E, Sanchez J, Nazarova AL, Zaidi SA, Jahan K, Katritch V, Canals M, Lane JR, Newman AH. Pharmacological and Physicochemical Properties Optimization for Dual-Target Dopamine D 3 (D 3R) and μ-Opioid (MOR) Receptor Ligands as Potentially Safer Analgesics. J Med Chem 2023; 66:10304-10341. [PMID: 37467430 PMCID: PMC11091828 DOI: 10.1021/acs.jmedchem.3c00417] [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] [Indexed: 07/21/2023]
Abstract
A new generation of dual-target μ opioid receptor (MOR) agonist/dopamine D3 receptor (D3R) antagonist/partial agonists with optimized physicochemical properties was designed and synthesized. Combining in vitro cell-based on-target/off-target affinity screening, in silico computer-aided drug design, and BRET functional assays, we identified new structural scaffolds that achieved high affinity and agonist/antagonist potencies for MOR and D3R, respectively, improving the dopamine receptor subtype selectivity (e.g., D3R over D2R) and significantly enhancing central nervous system multiparameter optimization scores for predicted blood-brain barrier permeability. We identified the substituted trans-(2S,4R)-pyrrolidine and trans-phenylcyclopropyl amine as key dopaminergic moieties and tethered these to different opioid scaffolds, derived from the MOR agonists TRV130 (3) or loperamide (6). The lead compounds 46, 84, 114, and 121 have the potential of producing analgesic effects through MOR partial agonism with reduced opioid-misuse liability via D3R antagonism. Moreover, the peripherally limited derivatives could have therapeutic indications for inflammation and neuropathic pain.
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Affiliation(s)
- Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Elizabeth Saab
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Julie Sanchez
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom
- Centre of Membrane Protein and Receptors, Universities of Birmingham and Nottingham, Midlands NG2 7AG, United Kingdom
| | - Antonina L. Nazarova
- Department of Quantitative and Computational Biology, Department of Chemistry, Dornsife Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, California 90089, United States
| | - Saheem A. Zaidi
- Department of Quantitative and Computational Biology, Department of Chemistry, Dornsife Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, California 90089, United States
| | - Khorshada Jahan
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, Department of Chemistry, Dornsife Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, California 90089, United States
| | - Meritxell Canals
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom
- Centre of Membrane Protein and Receptors, Universities of Birmingham and Nottingham, Midlands NG2 7AG, United Kingdom
| | - J. Robert Lane
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom
- Centre of Membrane Protein and Receptors, Universities of Birmingham and Nottingham, Midlands NG2 7AG, United Kingdom
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
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8
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Attram HD, Korkor CM, Taylor D, Njoroge M, Chibale K. Antimalarial Imidazopyridines Incorporating an Intramolecular Hydrogen Bonding Motif: Medicinal Chemistry and Mechanistic Studies. ACS Infect Dis 2023; 9:928-942. [PMID: 36946433 PMCID: PMC10111423 DOI: 10.1021/acsinfecdis.2c00584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
We previously identified a novel class of antimalarial benzimidazoles incorporating an intramolecular hydrogen bonding motif. The frontrunner of the series, analogue A, showed nanomolar activity against the chloroquine-sensitive NF54 and multi-drug-resistant K1 strains of Plasmodium falciparum (PfNF54 IC50 = 0.079 μM; PfK1 IC50 = 0.335 μM). Here, we describe a cell-based medicinal chemistry structure-activity relationship study using compound A as a basis. This effort led to the identification of novel antimalarial imidazopyridines with activities of <1 μM, favorable cytotoxicity profiles, and good physicochemical properties. Analogue 14 ( PfNF54 IC50 = 0.08 μM; PfK1 IC50 = 0.10 μM) was identified as the frontrunner of the series. Preliminary mode of action studies employing molecular docking, live-cell confocal microscopy, and a cellular heme fractionation assay revealed that 14 does not directly inhibit the conversion of heme to hemozoin, although it could be involved in other processes in the parasite's digestive vacuole.
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Affiliation(s)
- Henrietta D Attram
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Constance M Korkor
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Dale Taylor
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Mathew Njoroge
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
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9
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Oguma T, Uehara S, Nakahara K, Okuyama Y, Fuchino K, Suzuki N, Kan Y, Kanegawa N, Ogata Y, Kusakabe KI. A Quantum Mechanics-Based Method to Predict Intramolecular Hydrogen Bond Formation Reflecting P-glycoprotein Recognition. ACS Med Chem Lett 2023; 14:223-228. [PMID: 36793434 PMCID: PMC9923834 DOI: 10.1021/acsmedchemlett.2c00427] [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: 09/21/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023] Open
Abstract
Passive membrane permeability and an active transport process are key determinants for penetrating the blood-brain barrier. P-glycoprotein (P-gp), a well-known transporter, serves as the primary gatekeeper, having broad substrate specificity. A strategy to increase passive permeability and impair P-gp recognition is intramolecular hydrogen bonding (IMHB). 3 is a potent brain penetrant BACE1 inhibitor with high permeability and low P-gp recognition, although slight modifications to its tail amide group significantly affect P-gp efflux. We hypothesized that the difference in the propensity to form IMHB could impact P-gp recognition. Single-bond rotation at the tail group enables both IMHB forming and unforming conformations. We developed a quantum-mechanics-based method to predict IMHB formation ratios (IMHBRs). In a given data set, IMHBRs accounted for the corresponding temperature coefficients measured in NMR experiments, correlating with P-gp efflux ratios. Furthermore, the method was applied in hNK2 receptor antagonists, demonstrating that the IMHBR could be applied to other drug targets involving IMHB.
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Affiliation(s)
- Takuya Oguma
- Laboratory
for Medicinal Chemistry Research and Laboratory for Drug Discovery and
Development, Shionogi Pharmaceutical Research
Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Shota Uehara
- Laboratory
for Medicinal Chemistry Research and Laboratory for Drug Discovery and
Development, Shionogi Pharmaceutical Research
Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Kenji Nakahara
- Laboratory
for Medicinal Chemistry Research and Laboratory for Drug Discovery and
Development, Shionogi Pharmaceutical Research
Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Yuya Okuyama
- Laboratory
for Medicinal Chemistry Research and Laboratory for Drug Discovery and
Development, Shionogi Pharmaceutical Research
Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Kouki Fuchino
- Laboratory
for Medicinal Chemistry Research and Laboratory for Drug Discovery and
Development, Shionogi Pharmaceutical Research
Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Naoyuki Suzuki
- Laboratory
for Medicinal Chemistry Research and Laboratory for Drug Discovery and
Development, Shionogi Pharmaceutical Research
Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Yukiko Kan
- Laboratory
for Medicinal Chemistry Research and Laboratory for Drug Discovery and
Development, Shionogi Pharmaceutical Research
Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Naoki Kanegawa
- Laboratory
for Medicinal Chemistry Research and Laboratory for Drug Discovery and
Development, Shionogi Pharmaceutical Research
Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Yuki Ogata
- Laboratory
for Medicinal Chemistry Research and Laboratory for Drug Discovery and
Development, Shionogi Pharmaceutical Research
Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Ken-ichi Kusakabe
- Laboratory
for Medicinal Chemistry Research and Laboratory for Drug Discovery and
Development, Shionogi Pharmaceutical Research
Center, 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
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10
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Lim MA, Yang S, Mai H, Cheng AC. Exploring Deep Learning of Quantum Chemical Properties for Absorption, Distribution, Metabolism, and Excretion Predictions. J Chem Inf Model 2022; 62:6336-6341. [PMID: 35758421 DOI: 10.1021/acs.jcim.2c00245] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Quantum mechanical (QM) descriptors of small molecules have wide applicability in understanding organic reactivity and molecular properties, but the substantial compute cost required for ab initio QM calculations limits their broad usage. Here, we investigate the use of deep learning for predicting QM descriptors, with the goal of enabling usage of near-QM accuracy electronic properties on large molecular data sets such as those seen in drug discovery. Several deep learning approaches have previously been benchmarked on a published data set called QM9, where 12 ground-state properties have been calculated for molecules with up to nine heavy atoms, limited to C, H, N, O, and F elements. To advance the work beyond the QM9 chemical space and enable application to molecules encountered in drug discovery, we extend the QM9 data set by creating a QM9-extended data set covering an additional ∼20,000 molecules containing S and Cl atoms. Using this extended set, we generate new deep learning models as well as leverage ANI-2x models to provide predictions on larger, more diverse molecules common in drug discovery, and we find the models estimate 11 of 12 ground-state properties reasonably. We use the predicted QM descriptors to augment graph convolutional neural network (GCNN) models for selected ADME end points (rat microsomal clearance, hepatic clearance, total clearance, and P-glycoprotein efflux) and found varying degrees of performance improvement compared to nonaugmented GCNN models, including pronounced improvement in P-glycoprotein efflux prediction.
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Affiliation(s)
- Megan A Lim
- Computational and Structural Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Song Yang
- Computational and Structural Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Huanghao Mai
- Computational and Structural Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Alan C Cheng
- Computational and Structural Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
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11
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Li H, Yang H, Zhou M, Wei T, Zhou Y. Synergistic Effects of IMX-104 Components in Membrane Absorption: A Computational Study. ACS OMEGA 2022; 7:40892-40899. [PMID: 36406561 PMCID: PMC9670098 DOI: 10.1021/acsomega.2c03886] [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: 06/21/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
New insensitive munitions such as IMX-104 formulations are being developed to improve the safety suffering from accidental stimulations. Experimental data indicated the synergistic toxicity of 2,4-dinitroanisole (DNAN) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in IMX-104, which increased the concern about its environmental and health threats. Indeed, little is known about the synergistic mechanism. Here, we investigated the membrane absorption of DNAN and RDX as the first step toward uncovering synergistic toxicity. The permeability coefficient, transmembrane time, and liposome-water partition coefficient were calculated by the umbrella sampling technique. The results show that component RDX in the IMX-104 formulation promotes the membrane absorption of another more toxic component DNAN, suggesting that the synergistic toxicity effect of IMX-104 may emerge from their membrane adsorption stage. In detail, the integrating free-energy curves show that DNAN, RDX, or their mixture in membranes would promote subsequent molecules passing through membranes. For the mixture of DNAN and RDX, RDX was absorbed by the membrane before DNAN. Postabsorbed DNAN tends to stay around RDX, which is due to the strong van der Waals (VDW) interaction between them. RDX stabilized under phospholipid headgroups limits the overflow of DNAN from the membrane, which results in 11% more absorption of DNAN by the membrane than in the case of the pure DNAN system.
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12
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Sousa CF, Kamal MAM, Richter R, Elamaldeniya K, Hartmann RW, Empting M, Lehr CM, Kalinina OV. Modeling the Effect of Hydrophobicity on the Passive Permeation of Solutes across a Bacterial Model Membrane. J Chem Inf Model 2022; 62:5023-5033. [PMID: 36214845 DOI: 10.1021/acs.jcim.2c00767] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Passive diffusion across biomembranes is an important mechanism of permeation for multiple drugs, including antibiotics. However, this process is frequently neglected while studying drug uptake and, in our view, warrants further investigation. Here, we apply molecular dynamics simulations to investigate the impact of changes in molecular hydrophobicity on the permeability of a series of inhibitors of the quorum sensing of Pseudomonas aeruginosa, previously discovered by us, across a membrane model. Overall, we show that permeation across this membrane model does not correlate with the molecule's hydrophobicity. We demonstrate that using a simple model for permeation, based on the difference between the maximum and minimum of the free energy profile, outperforms the inhomogeneous solubility-diffusion model, yielding a permeability ranking that better agrees with the experimental results, especially for hydrophobic permeants. The calculated differences in permeability could not explain differences in in bacterio activity. Nevertheless, substantial differences in molecular orientation along the permeation pathway correlate with the in bacterio activity, emphasizing the importance of analyzing, at an atomistic level, the permeation pathway of these solutes.
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Affiliation(s)
- Carla F Sousa
- Drug Bioinformatics Group, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany
| | - Mohamed A M Kamal
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Department of Pharmacy, Saarland University, Saarbrücken66123, Germany
| | - Robert Richter
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany
| | - Kalanika Elamaldeniya
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Center for Bioinformatics, Saarland University, Saarbrücken66123, Germany
| | - Rolf W Hartmann
- Department of Pharmacy, Saarland University, Saarbrücken66123, Germany.,German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig, Saarbrücken66123, Germany.,Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken66123, Germany
| | - Martin Empting
- Department of Pharmacy, Saarland University, Saarbrücken66123, Germany.,Antiviral & Antivirulence Drugs Group, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig, Saarbrücken66123, Germany
| | - Claus-Michael Lehr
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Department of Pharmacy, Saarland University, Saarbrücken66123, Germany
| | - Olga V Kalinina
- Drug Bioinformatics Group, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Center for Bioinformatics, Saarland University, Saarbrücken66123, Germany.,Medical Faculty, Saarland University, Homburg66421, Germany
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13
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Reliable Prediction of Caco-2 Permeability by Supervised Recursive Machine Learning Approaches. Pharmaceutics 2022; 14:pharmaceutics14101998. [PMID: 36297432 PMCID: PMC9610902 DOI: 10.3390/pharmaceutics14101998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
The heterogeneity of the Caco-2 cell line and differences in experimental protocols for permeability assessment using this cell-based method have resulted in the high variability of Caco-2 permeability measurements. These problems have limited the generation of large datasets to develop accurate and applicable regression models. This study presents a QSPR approach developed on the KNIME analytical platform and based on a structurally diverse dataset of over 4900 molecules. Interpretable models were obtained using random forest supervised recursive algorithms for data cleaning and feature selection. The development of a conditional consensus model based on regional and global regression random forest produced models with RMSE values between 0.43–0.51 for all validation sets. The potential applicability of the model as a surrogate for the in vitro Caco-2 assay was demonstrated through blind prediction of 32 drugs recommended by the International Council for the Harmonization of Technical Requirements for Pharmaceuticals (ICH) for validation of in vitro permeability methods. The model was validated for the preliminary estimation of the BCS/BDDCS class. The KNIME workflow developed to automate new drug prediction is freely available. The results suggest that this automated prediction platform is a reliable tool for identifying the most promising compounds with high intestinal permeability during the early stages of drug discovery.
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14
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Agarwal P, Huckle J, Newman J, Reid DL. Trends in small molecule drug properties: A developability molecule assessment perspective. Drug Discov Today 2022; 27:103366. [PMID: 36122862 DOI: 10.1016/j.drudis.2022.103366] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/10/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022]
Abstract
Developability molecule assessment is a key interfacial capability across the biopharmaceutical industry, screening and staging molecules discovered by medicinal chemists for successful chemistry manufacturing controls (CMC) development and launch. The breadth of responsibility and expertise such teams possess puts them in a unique position to understand the impact of the physicochemical properties of a drug during its initial discovery and subsequent development. However, most of the publications describing trends in physicochemical properties are written from a medicinal chemistry perspective with the aim to identify molecules with better ADMET profiles that are either lead-like or drug-like, failing to describe the impact these properties have on CMC development. To systematically uncover knowledge obtained from recent trends in physicochemical properties and the corresponding impact on CMC development, a comprehensive analysis was conducted on molecules in the drug repurposing hub dataset. The only physicochemical property that seems to have been preserved in FDA-approved oral molecules over the decades (1900-2020) is a constant H-bond donor count, highlighting the importance this property has on cell permeability and lattice energy. Pharmaceutical attrition analysis suggests that partition-distribution coefficient, H-bond acceptors, polar surface area and the fraction of sp3 carbons are properties that are associated with compound attrition. Looking at pharmaceutical attrition asynchronously with the temporal analysis of FDA-approved oral molecules highlights the opposing trends, risks and diminishing effects some of these physiochemical properties (cLogP, cLogD and Fsp3) have on describing compound attrition during the past decade. Trellising the dataset by target class suggests that certain formulation and drug delivery strategies can be anticipated or put into place based on target class of a molecule. For example, molecules binding to nuclear hormone receptors are amenable to lipid-based drug delivery systems with proven commercial success. Although the poor solubility of kinase inhibitors is a combination of hydrophobicity (due to aromaticity) required to bind to its target and high lattice energy (melting point), they are a challenging target class to formulate. The influence of drug targets on physicochemical properties and the temporal nature of these properties is highlighted when comparing molecules in the drug repurposing dataset to those developed at Amgen. An improved understanding of the impact of molecular properties on performance attributes can accelerate decisions and facilitate risk assessments during candidate selection and development.
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Affiliation(s)
- Prashant Agarwal
- Drug Product Technologies, Process Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA.
| | - James Huckle
- Drug Product Technologies, Process Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Jake Newman
- Drug Product Technologies, Process Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Darren L Reid
- Drug Product Technologies, Process Development, Amgen, 360 Binney St, Cambridge, MA 02142, USA.
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15
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Meanwell NA, Loiseleur O. Applications of Isosteres of Piperazine in the Design of Biologically Active Compounds: Part 1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10942-10971. [PMID: 35675050 DOI: 10.1021/acs.jafc.2c00726] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Piperazine and homopiperazine are well-studied heterocycles in drug design that have found gainful application as scaffolds and terminal elements and for enhancing the aqueous solubility of a molecule. The optimization of drug candidates that incorporate these heterocycles in an effort to refine potency, selectivity, and developability properties has stimulated the design and evaluation of a wide range of bioisosteres that can offer advantage. In this review, we summarize the design and application of bioisosteres of piperazine and homopiperazine that have almost exclusively been in the drug design arena. While there are ∼100 approved drugs that incorporate a piperazine ring, only a single marketed agricultural product is built on this heterocycle. As part of the review, we discuss some of the potential reasons underlying the relatively low level of importance of this heterocycle to the design of agrochemicals and highlight the potential opportunities for their use in contemporary research programs.
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Affiliation(s)
- Nicholas A Meanwell
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey 08543, United States
| | - Olivier Loiseleur
- Syngenta Crop Protection Research, Schaffhauserstrasse, Stein CH-4332, Switzerland
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16
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Argikar U, Blatter M, Bednarczyk D, Chen Z, Cho YS, Doré M, Dumouchel JL, Ho S, Hoegenauer K, Kawanami T, Mathieu S, Meredith E, Möbitz H, Murphy SK, Parthasarathy S, Soldermann CP, Santos J, Silver S, Skolnik S, Stojanovic A. Paradoxical Increase of Permeability and Lipophilicity with the Increasing Topological Polar Surface Area within a Series of PRMT5 Inhibitors. J Med Chem 2022; 65:12386-12402. [PMID: 36069672 DOI: 10.1021/acs.jmedchem.2c01068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An imidazolone → triazolone replacement addressed the limited passive permeability of a series of protein arginine methyl transferase 5 (PRMT5) inhibitors. This increase in passive permeability was unexpected given the increase in the hydrogen bond acceptor (HBA) count and topological polar surface area (TPSA), two descriptors that are typically inversely correlated with permeability. Quantum mechanics (QM) calculations revealed that this unusual effect was due to an electronically driven disconnect between TPSA and 3D-PSA, which manifests in a reduction in overall HBA strength as indicated by the HBA moment descriptor from COSMO-RS (conductor-like screening model for real solvation). HBA moment was subsequently deployed as a design parameter leading to the discovery of inhibitors with not only improved passive permeability but also reduced P-glycoprotein (P-gp) transport. Our case study suggests that hidden polarity as quantified by TPSA-3DPSA can be rationally designed through QM calculations.
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Affiliation(s)
- Upendra Argikar
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Blatter
- Novartis Institutes for BioMedical Research, Basel 4002, Switzerland
| | - Dallas Bednarczyk
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Zhuoliang Chen
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Young Shin Cho
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Michaël Doré
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Jennifer L Dumouchel
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Samuel Ho
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | | | - Toshio Kawanami
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Simon Mathieu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Erik Meredith
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Henrik Möbitz
- Novartis Institutes for BioMedical Research, Basel 4002, Switzerland
| | - Stephen K Murphy
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | | | | | - Jobette Santos
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Serena Silver
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Suzanne Skolnik
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
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17
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Hawryluk N, Robinson D, Shen Y, Kyne G, Bedore M, Menon S, Canan S, von Geldern T, Townson S, Gokool S, Ehrens A, Koschel M, Lhermitte-Vallarino N, Martin C, Hoerauf A, Hernandez G, Dalvie D, Specht S, Hübner MP, Scandale I. Discovery of Substituted Di(pyridin-2-yl)-1,2,4-thiadiazol-5-amines as Novel Macrofilaricidal Compounds for the Treatment of Human Filarial Infections. J Med Chem 2022; 65:11388-11403. [PMID: 35972896 PMCID: PMC9421654 DOI: 10.1021/acs.jmedchem.2c00960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Filarial diseases, including lymphatic filariasis and onchocerciasis, are considered among the most devastating of all tropical diseases, affecting about 145 million people worldwide. Efforts to control and eliminate onchocerciasis are impeded by a lack of effective treatments that target the adult filarial stage. Herein, we describe the discovery of a series of substituted di(pyridin-2-yl)-1,2,4-thiadiazol-5-amines as novel macrofilaricides for the treatment of human filarial infections.
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Affiliation(s)
- Natalie Hawryluk
- Bristol Myers Squibb, San Diego, California 92121, United States
| | - Dale Robinson
- Bristol Myers Squibb, San Diego, California 92121, United States
| | - Yixing Shen
- Bristol Myers Squibb, San Diego, California 92121, United States
| | - Graham Kyne
- Zoetis, Kalamazoo, Michigan 49001, United States
| | | | - Sanjay Menon
- Zoetis, Kalamazoo, Michigan 49001, United States
| | - Stacie Canan
- Bristol Myers Squibb, San Diego, California 92121, United States
| | | | - Simon Townson
- Northwick Park Institute for Medical Research, London HA1 3UJ, UK
| | - Suzanne Gokool
- Northwick Park Institute for Medical Research, London HA1 3UJ, UK
| | - Alexandra Ehrens
- Institute for Medical Microbiology, Immunology & Parasitology, University Hospital Bonn, 53127 Bonn, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, 53127 Bonn, Germany
| | - Marianne Koschel
- Institute for Medical Microbiology, Immunology & Parasitology, University Hospital Bonn, 53127 Bonn, Germany
| | - Nathaly Lhermitte-Vallarino
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum national d'Histoire Naturelle, Paris 75005, France
| | - Coralie Martin
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum national d'Histoire Naturelle, Paris 75005, France
| | - Achim Hoerauf
- Institute for Medical Microbiology, Immunology & Parasitology, University Hospital Bonn, 53127 Bonn, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, 53127 Bonn, Germany
| | | | - Deepak Dalvie
- Bristol Myers Squibb, San Diego, California 92121, United States
| | - Sabine Specht
- Institute for Medical Microbiology, Immunology & Parasitology, University Hospital Bonn, 53127 Bonn, Germany.,Drugs for Neglected Diseases Initiative, Geneva 1204, Switzerland
| | - Marc Peter Hübner
- Institute for Medical Microbiology, Immunology & Parasitology, University Hospital Bonn, 53127 Bonn, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, 53127 Bonn, Germany
| | - Ivan Scandale
- Drugs for Neglected Diseases Initiative, Geneva 1204, Switzerland
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18
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Silva AM, Martins-Gomes C, Ferreira SS, Souto EB, Andreani T. Molecular Physicochemical Properties of Selected Pesticides as Predictive Factors for Oxidative Stress and Apoptosis-Dependent Cell Death in Caco-2 and HepG2 Cells. Int J Mol Sci 2022; 23:ijms23158107. [PMID: 35897683 PMCID: PMC9331544 DOI: 10.3390/ijms23158107] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
In this work, three pesticides of different physicochemical properties: glyphosate (GLY, herbicide), imidacloprid (IMD, insecticide), and imazalil (IMZ, fungicide), were selected to assess their cytotoxicity against Caco-2 and HepG2 cells. Cell viability was assessed by the Alamar Blue assay, after 24 and 48 h exposure to different concentrations, and IC50 values were calculated. The mechanisms underlying toxicity, namely cellular reactive oxygen species (ROS), glutathione (GSH) content, lipid peroxidation, loss of mitochondrial membrane potential (MMP), and apoptosis/necrosis induction were assessed by flow cytometry. Cytotoxic profiles were further correlated with the molecular physicochemical parameters of pesticides, namely: water solubility, partition coefficient in an n-octanol/water (Log Pow) system, topological polar surface area (TPSA), the number of hydrogen-bonds (donor/acceptor), and rotatable bonds. In vitro outputs resulted in the following toxicity level: IMZ (Caco-2: IC50 = 253.5 ± 3.37 μM, and HepG2: IC50 = 94 ± 12 μM) > IMD (Caco-2: IC50 > 1 mM and HepG2: IC50 = 624 ± 24 μM) > GLY (IC50 >>1 mM, both cell lines), after 24 h treatment, being toxicity time-dependent (lower IC50 values at 48 h). Toxicity is explained by oxidative stress, as IMZ induced a higher intracellular ROS increase and lipid peroxidation, followed by IMD, while GLY did not change these markers. However, the three pesticides induced loss of MMP in HepG2 cells while in Caco-2 cells only IMZ produced significant MMP loss. Increased ROS and loss of MMP promoted apoptosis in Caco-2 cells subjected to IMZ, and in HepG2 cells exposed to IMD and IMZ, as assessed by Annexin-V/PI. The toxicity profile of pesticides is directly correlated with their Log Pow, as affinity for the lipophilic environment favours interaction with cell membranes governs, and is inversely correlated with their TPSA; however, membrane permeation is favoured by lower TPSA. IMZ presents the best molecular properties for membrane interaction and cell permeation, i.e., higher Log Pow, lower TPSA and lower hydrogen-bond (H-bond) donor/acceptor correlating with its higher toxicity. In conclusion, molecular physicochemical factors such as Log Pow, TPSA, and H-bond are likely to be directly correlated with pesticide-induced toxicity, thus they are key factors to potentially predict the toxicity of other compounds.
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Affiliation(s)
- Amélia M. Silva
- Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal; (C.M.-G.); (S.S.F.)
- Center for Research and Technology of Agro-Environmental and Biological Sciences (CITAB-UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal;
- Correspondence: ; Tel.: +351-259-350-921
| | - Carlos Martins-Gomes
- Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal; (C.M.-G.); (S.S.F.)
- Center for Research and Technology of Agro-Environmental and Biological Sciences (CITAB-UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal;
| | - Sandrine S. Ferreira
- Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal; (C.M.-G.); (S.S.F.)
- Center for Research and Technology of Agro-Environmental and Biological Sciences (CITAB-UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal;
| | - Eliana B. Souto
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- UCIBIO/REQUIMTE, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Tatiana Andreani
- Center for Research and Technology of Agro-Environmental and Biological Sciences (CITAB-UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal;
- GreenUPorto—Sustainable Agrifood Production Research Centre and Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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19
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Silva AM, Martins-Gomes C, Silva TL, Coutinho TE, Souto EB, Andreani T. In Vitro Assessment of Pesticides Toxicity and Data Correlation with Pesticides Physicochemical Properties for Prediction of Toxicity in Gastrointestinal and Skin Contact Exposure. TOXICS 2022; 10:toxics10070378. [PMID: 35878283 PMCID: PMC9317861 DOI: 10.3390/toxics10070378] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023]
Abstract
In this work, three pesticides of different physicochemical properties, namely, glyphosate (herbicide), imidacloprid (insecticide) and imazalil (fungicide), were selected to assess their cytotoxicity against distinct cell models (Caco-2, HepG2, A431, HaCaT, SK-MEL-5 and RAW 264.7 cells) to mimic gastrointestinal and skin exposure with potential systemic effect. Cells were subjected to different concentrations of selected pesticides for 24 h or 48 h. Cell viability was assessed by Alamar Blue assay, morphological changes by bright-field microscopy and the IC50 values were calculated. Cytotoxic profiles were analysed using the physico-chemical parameters of the pesticides, namely: molecular weight, water solubility, the partition coefficient in the n-octanol/water (Log Pow) system, the topological polar surface area (TPSA), and number of hydrogen-bonds (donor/acceptor) and rotatable bonds. Results showed that glyphosate did not reduce cell viability (up to 1 mM), imidacloprid induced moderate toxicity (IC50 > 1 mM for Caco-2 cells while IC50 = 305.9 ± 22.4 μM for RAW 264.7 cells) and imazalil was highly cytotoxic (IC50 > 253.5 ± 3.37 for Caco-2 cells while IC50 = 31.3 ± 2.7 μM for RAW 264.7 cells) after 24 h exposure. Toxicity was time-dependent as IC50 values at 48 h exposure were lower, and decrease in cell viability was accompanied by changes in cell morphology. Pesticides toxicity was found to be directly proportional with their Log Pow, indicating that the affinity to a lipophilic environment such as the cell membranes governs their toxicity. Toxicity is inverse to pesticides TPSA, but lower TPSA favours membrane permeation. The lower toxicity against Caco-2 cells was attributed to the physiology and metabolism of cell barriers equipped with various ABC transporters. In conclusion, physicochemical factors such as Log Pow, TPSA and H-bond are likely to be directly correlated with pesticide-induced toxicity, thus being key factors to potentially predict the toxicity of other compounds.
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Affiliation(s)
- Amélia M. Silva
- Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal; (C.M.-G.); (T.L.S.); (T.E.C.)
- Center for Research and Technology of Agro-Environmental and Biological Sciences (CITAB-UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal;
- Correspondence: ; Tel.: +351-259-350-921
| | - Carlos Martins-Gomes
- Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal; (C.M.-G.); (T.L.S.); (T.E.C.)
- Center for Research and Technology of Agro-Environmental and Biological Sciences (CITAB-UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal;
| | - Tânia L. Silva
- Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal; (C.M.-G.); (T.L.S.); (T.E.C.)
- Center for Research and Technology of Agro-Environmental and Biological Sciences (CITAB-UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal;
| | - Tiago E. Coutinho
- Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal; (C.M.-G.); (T.L.S.); (T.E.C.)
- Center for Research and Technology of Agro-Environmental and Biological Sciences (CITAB-UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal;
| | - Eliana B. Souto
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- UCIBIO/REQUIMTE, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Tatiana Andreani
- Center for Research and Technology of Agro-Environmental and Biological Sciences (CITAB-UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal;
- GreenUPorto—Sustainable Agrifood Production Research Centre & Department of Biology, Faculty of Sciences of the University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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20
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Fairhurst RA, Furet P, Imbach-Weese P, Stauffer F, Rueeger H, McCarthy C, Ripoche S, Oswald S, Arnaud B, Jary A, Maira M, Schnell C, Guthy DA, Wartmann M, Kiffe M, Desrayaud S, Blasco F, Widmer T, Seiler F, Gutmann S, Knapp M, Caravatti G. Identification of NVP-CLR457 as an Orally Bioavailable Non-CNS-Penetrant pan-Class IA Phosphoinositol-3-Kinase Inhibitor. J Med Chem 2022; 65:8345-8379. [PMID: 35500094 DOI: 10.1021/acs.jmedchem.2c00267] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Balanced pan-class I phosphoinositide 3-kinase inhibition as an approach to cancer treatment offers the prospect of treating a broad range of tumor types and/or a way to achieve greater efficacy with a single inhibitor. Taking buparlisib as the starting point, the balanced pan-class I PI3K inhibitor 40 (NVP-CLR457) was identified with what was considered to be a best-in-class profile. Key to the optimization to achieve this profile was eliminating a microtubule stabilizing off-target activity, balancing the pan-class I PI3K inhibition profile, minimizing CNS penetration, and developing an amorphous solid dispersion formulation. A rationale for the poor tolerability profile of 40 in a clinical study is discussed.
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Affiliation(s)
- Robin A Fairhurst
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Pascal Furet
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | | | - Frédéric Stauffer
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Heinrich Rueeger
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Clive McCarthy
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Sebastien Ripoche
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Susanne Oswald
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Bertrand Arnaud
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Aline Jary
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Michel Maira
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Christian Schnell
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Daniel A Guthy
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Markus Wartmann
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Michael Kiffe
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | | | - Francesca Blasco
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Toni Widmer
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Frank Seiler
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Sascha Gutmann
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Mark Knapp
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Giorgio Caravatti
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
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21
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Ntungwe EN, Stojanov SJ, Duarte NM, Candeias NR, Díaz-Lanza AM, Vágvölgyi M, Hunyadi A, Pešić M, Rijo P. C 20- nor-Abietane and Three Abietane Diterpenoids from Plectranthus mutabilis Leaves as P-Glycoprotein Modulators. ACS Med Chem Lett 2022; 13:674-680. [PMID: 35450348 PMCID: PMC9014510 DOI: 10.1021/acsmedchemlett.1c00711] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/04/2022] [Indexed: 01/05/2023] Open
Abstract
In this study, a bioguided fractionation of Plectranthus mutabilis extract was performed by chromatographic methods. It yielded one new nor-abietane diterpene, mutabilol (1), and three known abietanes, coleon-U-quinone (2), 8α,9α-epoxycoleon-U-quinone (3), and coleon U (4). The abietane diterpenoid 5 was also tentatively identified using HPLC-MS/MS. Moreover, the extract profile and quantification of each isolated compound were determined by HPLC-DAD. Compound 4 was the major compound in the extract. Compounds 2-4 were found to be selective toward cancer cell lines and were able to inhibit P-glycoprotein (P-gp) activity in NCI-H460/R cells at longer exposure of 72 h and consequently revert doxorubicin (DOX) resistance in subsequent combined treatment. None of the compounds influenced the P-gp expression in NCI-H460/R cells, while the extract significantly increased it.
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Affiliation(s)
- Epole N. Ntungwe
- CBIOS─Research Center for Biosciences & Health Technologies, Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisbon, Portugal
- Pharmacology Area (Pharmacognosy Laboratory), New Antitumor Compounds: Toxic Action on Leukemia Cells Research Group, Faculty of Pharmacy, Department of Biomedical Sciences, University of Alcalá de Henares, Ctra. A2, Km 33.100−Campus Universitario, 28805 Alcalá de Henares, Spain
| | - Sofija Jovanović Stojanov
- Institute for Biological Research “Siniša Stanković”─National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Noélia M. Duarte
- Research Institute for Medicines (iMED.Ulisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Nuno R. Candeias
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33101 Tampere, Finland
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ana M. Díaz-Lanza
- Pharmacology Area (Pharmacognosy Laboratory), New Antitumor Compounds: Toxic Action on Leukemia Cells Research Group, Faculty of Pharmacy, Department of Biomedical Sciences, University of Alcalá de Henares, Ctra. A2, Km 33.100−Campus Universitario, 28805 Alcalá de Henares, Spain
| | - Máté Vágvölgyi
- Institute of Pharmacognosy, Interdisciplinary Excellence Centre, University of Szeged, Eötvös str. 6, 6720 Szeged, Hungary
| | - Attila Hunyadi
- Institute of Pharmacognosy, Interdisciplinary Excellence Centre, University of Szeged, Eötvös str. 6, 6720 Szeged, Hungary
| | - Milica Pešić
- Institute for Biological Research “Siniša Stanković”─National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Patrícia Rijo
- CBIOS─Research Center for Biosciences & Health Technologies, Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisbon, Portugal
- Research Institute for Medicines (iMED.Ulisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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22
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Slater O, Kontoyianni M. A computational study of somatostatin subtype-4 receptor agonist binding. SN APPLIED SCIENCES 2022. [DOI: 10.1007/s42452-022-04968-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
AbstractThe somatostatin subtype-4 receptor (sst4) is highly expressed in neocortical and hippocampal areas, which are affected by amyloid beta accumulation. Sst4 agonists enhance downstream activity of amyloid beta peptide catabolism through neprilysin and may slow the progression of Alzheimer’s disease (AD). Sst4 is a G protein coupled receptor (GPCR), the structure of which has yet to be resolved. A newly constructed sst4 homology model, along with a previously reported model-built sst4 receptor structure, were used in the present study to gain insights into binding requirements of sst4 agonists employing a set of compounds patented by Boehringer Ingelheim. Besides aiming at delineating binding at the macromolecular level of these recently disclosed compounds, our objectives included the generation of a quantitative structure-activity relationship (QSAR) global model to explore the relationship between chemical structure and affinity. Through the implementation of model building, docking, and QSAR, plausible correlations between structural properties and the binding affinity are established. This study sheds light on understanding binding requirements at the sst4 receptor.
Graphical abstract
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23
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Liang R, Tomita D, Sasaki Y, Ginn J, Michino M, Huggins DJ, Baxt L, Kargman S, Shahid M, Aso K, Duggan M, Stamford AW, DeStanchina E, Liverton N, Meinke PT, Foley MA, Phillips RE. A Chemical Strategy toward Novel Brain-Penetrant EZH2 Inhibitors. ACS Med Chem Lett 2022; 13:377-387. [PMID: 35300079 PMCID: PMC8919293 DOI: 10.1021/acsmedchemlett.1c00448] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022] Open
Abstract
Aberrant gene-silencing through dysregulation of polycomb protein activity has emerged as an important oncogenic mechanism in cancer, implicating polycomb proteins as important therapeutic targets. Recently, an inhibitor targeting EZH2, the methyltransferase component of PRC2, received U.S. Food and Drug Administration approval following promising clinical responses in cancer patients. However, the current array of EZH2 inhibitors have poor brain penetrance, limiting their use in patients with central nervous system malignancies, a number of which have been shown to be sensitive to EZH2 inhibition. To address this need, we have identified a chemical strategy, based on computational modeling of pyridone-containing EZH2 inhibitor scaffolds, to minimize P-glycoprotein activity, and here we report the first brain-penetrant EZH2 inhibitor, TDI-6118 (compound 5). Additionally, in the course of our attempts to optimize this compound, we discovered TDI-11904 (compound 21), a novel, highly potent, and peripherally active EZH2 inhibitor based on a 7 member ring structure.
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Affiliation(s)
- Rui Liang
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, New York 10021, United States
| | - Daisuke Tomita
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, New York 10021, United States
| | - Yusuke Sasaki
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, New York 10021, United States
| | - John Ginn
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, New York 10021, United States
| | - Mayako Michino
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, New York 10021, United States
| | - David J Huggins
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, New York 10021, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10021, United States
| | - Leigh Baxt
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, New York 10021, United States
| | - Stacia Kargman
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, New York 10021, United States
| | - Maaz Shahid
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Epigenetics Program, Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States.,Abramson Cancer Center, Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Kazuyoshi Aso
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, New York 10021, United States
| | - Mark Duggan
- LifeSci Consulting, LLC., 18243 SE Ridgeview Drive, Tequesta, Florida 33469, United States
| | - Andrew W Stamford
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, New York 10021, United States
| | - Elisa DeStanchina
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Nigel Liverton
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, New York 10021, United States
| | - Peter T Meinke
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, New York 10021, United States.,Department of Pharmacology, Weill Cornell Medical College, New York, New York 10021, United States
| | - Michael A Foley
- Tri-Institutional Therapeutics Discovery Institute, 413 East 69th Street, New York, New York 10021, United States
| | - Richard E Phillips
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Epigenetics Program, Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States.,Abramson Cancer Center, Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
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24
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Wang X, Xiang J, Huang G, Kang L, Yang G, Wu H, Jiang K, Liang Z, Yang S. Inhibition of Podocytes DPP4 Activity Is a Potential Mechanism of Lobeliae Chinensis Herba in Treating Diabetic Kidney Disease. Front Pharmacol 2021; 12:779652. [PMID: 34950037 PMCID: PMC8688925 DOI: 10.3389/fphar.2021.779652] [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: 09/19/2021] [Accepted: 11/17/2021] [Indexed: 01/23/2023] Open
Abstract
Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease and has become a serious public health problem worldwide. Dipeptidyl peptidase-4 (DPP4) inhibitors, an emerging drug for the treatment of diabetes, have been found to have renoprotective effects in addition to glucose-lowering effects and therefore have the potential to be a treatment modality for DKD. Lobeliae Chinensis Herba (LCH), a traditional Chinese herb widely used in the treatment of diabetes, has recently been found to have a hypoglycaemic mechanism related to the inhibition of DPP4. Firstly, analysis of single-cell sequencing data from mouse kidneys in the National Center for Biotechnology Information (NCBI) database revealed that DPP4 was specifically upregulated in DKD podocytes and was associated with podocyte proliferation. Subsequently, the network pharmacology approach was applied to the screening of compounds. Twelve LCH active ingredients targeting DPP4 were extracted from the Traditional Chinese Medicine System Pharmacology (TCMSP) database. In addition, these 12 compounds and DPP4 were molecularly docked to predict the probability of them affecting DPP4 activity. In vitro, Quercetin, Methyl rosmarinate, Kaempferol, Diosmetin and Acacetin were demonstrated to retard podocyte proliferation by inhibiting DPP4 activity and were the top five compounds predicted by molecular docking to be the most likely to affect DPP4 activity. The half maximal inhibitory concentration (IC50) of the five compounds for DPP4 activity were as follows. Acacetin Log IC50 = −8.349, 95%CI (−9.266, −7.265), Diosmtrin Log IC50 = −8.419, 95%CI (−8.889, −7.950), Log IC50 = −8.349, 95%CI (−9.266, −7.265), Methyl rosmarinate Log IC50 = −8.415, 95%CI (−8.751, −8.085), Kaempferol Log IC50 = −8.297, 95%CI (−9.001, −7.615), Quercetin Log IC50 = −8.864, 95%CI (−9.107, −8.615). Finally, Quercetin, Methyl rosmarinate, Kaempferol, Diosmetin and Acacetin qualified for pharmacokinetic and drug similarity screening and have the potential to be the most promising oral agents for the treatment of DKD.
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Affiliation(s)
- Xinyu Wang
- Department of Geriatrics, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
| | - Jiaqing Xiang
- Department of Geriatrics, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
| | - Guixiao Huang
- The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Lin Kang
- Department of Geriatrics, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
| | - Guangyan Yang
- Department of Geriatrics, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
| | - Han Wu
- Department of Endocrinology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
| | - Kewei Jiang
- Department of Geriatrics, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
| | - Zhen Liang
- Department of Geriatrics, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
| | - Shu Yang
- Department of Geriatrics, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
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25
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Mammoliti O, Jansen K, El Bkassiny S, Palisse A, Triballeau N, Bucher D, Allart B, Jaunet A, Tricarico G, De Wachter M, Menet C, Blanc J, Letfus V, Rupčić R, Šmehil M, Poljak T, Coornaert B, Sonck K, Duys I, Waeckel L, Lecru L, Marsais F, Jagerschmidt C, Auberval M, Pujuguet P, Oste L, Borgonovi M, Wakselman E, Christophe T, Houvenaghel N, Jans M, Heckmann B, Sanière L, Brys R. Discovery and Optimization of Orally Bioavailable Phthalazone and Cinnolone Carboxylic Acid Derivatives as S1P2 Antagonists against Fibrotic Diseases. J Med Chem 2021; 64:14557-14586. [PMID: 34581584 DOI: 10.1021/acs.jmedchem.1c01066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease. Current treatments only slow down disease progression, making new therapeutic strategies compelling. Increasing evidence suggests that S1P2 antagonists could be effective agents against fibrotic diseases. Our compound collection was mined for molecules possessing substructure features associated with S1P2 activity. The weakly potent indole hit 6 evolved into a potent phthalazone series, bearing a carboxylic acid, with the aid of a homology model. Suboptimal pharmacokinetics of a benzimidazole subseries were improved by modifications targeting potential interactions with transporters, based on concepts deriving from the extended clearance classification system (ECCS). Scaffold hopping, as a part of a chemical enablement strategy, permitted the rapid exploration of the position adjacent to the carboxylic acid. Compound 38, with good pharmacokinetics and in vitro potency, was efficacious at 10 mg/kg BID in three different in vivo mouse models of fibrotic diseases in a therapeutic setting.
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Affiliation(s)
- Oscar Mammoliti
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Koen Jansen
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | | | - Adeline Palisse
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | | | - Denis Bucher
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Brigitte Allart
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Alex Jaunet
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | | | - Maxim De Wachter
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Christel Menet
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Javier Blanc
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Vatroslav Letfus
- Fidelta Ltd., Prilaz Baruna Filipovića 29, ZagrebHR-10000, Croatia
| | - Renata Rupčić
- Fidelta Ltd., Prilaz Baruna Filipovića 29, ZagrebHR-10000, Croatia
| | - Mario Šmehil
- Fidelta Ltd., Prilaz Baruna Filipovića 29, ZagrebHR-10000, Croatia
| | - Tanja Poljak
- Fidelta Ltd., Prilaz Baruna Filipovića 29, ZagrebHR-10000, Croatia
| | | | - Kathleen Sonck
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Inge Duys
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Ludovic Waeckel
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Lola Lecru
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Florence Marsais
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | | | - Marielle Auberval
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Philippe Pujuguet
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Line Oste
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Monica Borgonovi
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | | | | | | | - Mia Jans
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Bertrand Heckmann
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Laurent Sanière
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Reginald Brys
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
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26
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Zandona A, Maraković N, Mišetić P, Madunić J, Miš K, Padovan J, Pirkmajer S, Katalinić M. Activation of (un)regulated cell death as a new perspective for bispyridinium and imidazolium oximes. Arch Toxicol 2021; 95:2737-2754. [PMID: 34173857 DOI: 10.1007/s00204-021-03098-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/15/2021] [Indexed: 12/20/2022]
Abstract
Oximes, investigated as antidotes against organophosphates (OP) poisoning, are known to display toxic effects on a cellular level, which could be explained beyond action on acetylcholinesterase as their main target. To investigate this further, we performed an in vitro cell-based evaluation of effects of two structurally diverse oxime groups at concentrations of up to 800 μM, on several cell models: skeletal muscle, kidney, liver, and neural cells. As indicated by our results, compounds with an imidazolium core induced necrosis, unregulated cell death characterized by a cell burst, increased formation of reactive oxygen species, and activation of antioxidant scavenging. On the other hand, oximes with a pyridinium core activated apoptosis through specific caspases 3, 8, and/or 9. Interestingly, some of the compounds exhibited a synergistic effect. Moreover, we generated a pharmacophore model for each oxime series and identified ligands from public databases that map to generated pharmacophores. Several interesting hits were obtained including chemotherapeutics and specific inhibitors. We were able to define the possible structural features of tested oximes triggering toxic effects: chlorine atoms in combination with but-2(E)-en-1,4-diyl linker and adding a second benzene ring with substituents such as chlorine and/or methyl on the imidazolium core. Such oximes could not be used in further OP antidote development research, but could be introduced in other research studies on new specific targets. This could undoubtedly result in an overall improved wider use of unexplored oxime database created so far in OP antidotes field of research in a completely new perspective.
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Affiliation(s)
- Antonio Zandona
- Institute for Medical Research and Occupational Health, POB 291, 10001, Zagreb, Croatia
| | - Nikola Maraković
- Institute for Medical Research and Occupational Health, POB 291, 10001, Zagreb, Croatia
| | | | - Josip Madunić
- Institute for Medical Research and Occupational Health, POB 291, 10001, Zagreb, Croatia
| | - Katarina Miš
- Faculty of Medicine, Institute of Pathophysiology, University of Ljubljana, Ljubljana, Slovenia
| | | | - Sergej Pirkmajer
- Faculty of Medicine, Institute of Pathophysiology, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Katalinić
- Institute for Medical Research and Occupational Health, POB 291, 10001, Zagreb, Croatia.
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27
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Miller S, Blanco MJ. Small molecule therapeutics for neuroinflammation-mediated neurodegenerative disorders. RSC Med Chem 2021; 12:871-886. [PMID: 34223157 PMCID: PMC8221257 DOI: 10.1039/d1md00036e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Chronically activated microglia and the resulting cascade of neuroinflammatory mechanisms have been postulated to play a critical role in neurodegenerative disorders. Microglia are the main component of the brain's innate immune system and become activated by infection, injury, misfolded proteins or a multitude of other stimuli. Activated microglia release pro-inflammatory and cytotoxic factors that can damage neurons and transform astrocytes to become toxic to neurons as well. Therapeutic approaches aiming to modulate microglia activation may be beneficial to mitigate the progression of inflammatory-mediated neurodegenerative diseases. In this literature review, we provide an overview of recent progress on key microglia targets and discovery of small molecule compounds advancing in clinical trials to minimize neuroinflammation.
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Affiliation(s)
- Silke Miller
- Sage Therapeutics, Inc. 215 First Street Cambridge Massachusetts 02142 USA
| | - Maria-Jesus Blanco
- Sage Therapeutics, Inc. 215 First Street Cambridge Massachusetts 02142 USA
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28
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Girst G, Ötvös SB, Fülöp F, Balogh GT, Hunyadi A. Pharmacokinetics-Driven Evaluation of the Antioxidant Activity of Curcuminoids and Their Major Reduced Metabolites-A Medicinal Chemistry Approach. Molecules 2021; 26:molecules26123542. [PMID: 34200647 PMCID: PMC8229286 DOI: 10.3390/molecules26123542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/18/2022] Open
Abstract
Curcuminoids are the main bioactive components of the well-known Asian spice and traditional medicine turmeric. Curcuminoids have poor chemical stability and bioavailability; in vivo they are rapidly metabolized to a set of bioreduced derivatives and/or glucuronide and sulfate conjugates. The reduced curcuminoid metabolites were also reported to exert various bioactivities in vitro and in vivo. In this work, we aimed to perform a comparative evaluation of curcuminoids and their hydrogenated metabolites from a medicinal chemistry point of view, by determining a set of key pharmacokinetic parameters and evaluating antioxidant potential in relation to such properties.Reduced metabolites were prepared from curcumin and demethoxycurcumin through continuous-flow hydrogenation. As selected pharmacokinetic parameters, kinetic solubility, chemical stability, metabolic stability in human liver microsomes, and parallel artificial membrane permeability assay (PAMPA)-based gastrointestinal and blood-brain barrier permeability were determined. Experimentally determined logP for hydrocurcumins in octanol-water and toluene-water systems provided valuable data on the tendency for intramolecular hydrogen bonding by these compounds. Drug likeness of the compounds were further evaluated by a in silico calculations. Antioxidant properties in diphenyl-2-picrylhydrazyl (DPPH) radical scavenging and oxygen radical absorbance capacity (ORAC) assays were comparatively evaluated through the determination of ligand lipophilic efficiency (LLE). Our results showed dramatically increased water solubility and chemical stability for the reduced metabolites as compared to their corresponding parent compound. Hexahydrocurcumin was found the best candidate for drug development based on a complex pharmacokinetical comparison and high LLE values for its antioxidant properties. Development of tetrahydrocurcumin and tetrahydro-demethoxycurcumin would be limited by their very poor metabolic stability, therefore such an effort would rely on formulations bypassing first-pass metabolism.
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Affiliation(s)
- Gábor Girst
- Institute of Pharmacognosy, Interdisciplinary Centre of Excellence, University of Szeged, H-6720 Szeged, Hungary;
| | - Sándor B. Ötvös
- Institute of Pharmaceutical Chemistry, University of Szeged, H-6720 Szeged, Hungary; (S.B.Ö.); (F.F.)
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Ferenc Fülöp
- Institute of Pharmaceutical Chemistry, University of Szeged, H-6720 Szeged, Hungary; (S.B.Ö.); (F.F.)
| | - György T. Balogh
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
- Department of Pharmacodynamics and Biopharmacy, University of Szeged, H-6720 Szeged, Hungary
- Correspondence: (G.T.B.); (A.H.); Tel.: +36-1463-2174 (G.T.B.); +36-6254-6456 (A.H.)
| | - Attila Hunyadi
- Institute of Pharmacognosy, Interdisciplinary Centre of Excellence, University of Szeged, H-6720 Szeged, Hungary;
- Interdisciplinary Centre of Natural Products, University of Szeged, H-6720 Szeged, Hungary
- Correspondence: (G.T.B.); (A.H.); Tel.: +36-1463-2174 (G.T.B.); +36-6254-6456 (A.H.)
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29
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Synthesis and Characterization of Some New Quinoxalin-2( 1H)one and 2-Methyl-3 H-quinazolin-4-one Derivatives Targeting the Onset and Progression of CRC with SRA, Molecular Docking, and ADMET Analyses. Molecules 2021; 26:molecules26113121. [PMID: 34071141 PMCID: PMC8197120 DOI: 10.3390/molecules26113121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 01/09/2023] Open
Abstract
The pathogenesis of colorectal cancer is a multifactorial process. Dysbiosis and the overexpression of COX-2 and LDHA are important effectors in the initiation and development of the disease through chromosomal instability, PGE2 biosynthesis, and induction of the Warburg effect, respectively. Herein, we report the in vitro testing of some new quinoxalinone and quinazolinone Schiff’s bases as: antibacterial, COX-2 and LDHA inhibitors, and anticolorectal agents on HCT-116 and LoVo cells. Moreover, molecular docking and SAR analyses were performed to identify the structural features contributing to the biological activities. Among the synthesized molecules, the most active cytotoxic agent, (6d) was also a COX-2 inhibitor. In silico ADMET studies predicted that (6d) would have high Caco-2 permeability, and %HIA (99.58%), with low BBB permeability, zero hepatotoxicity, and zero risk of sudden cardiac arrest, or mutagenicity. Further, (6d) is not a potential P-gp substrate, instead, it is a possible P-gpI and II inhibitor, therefore, it can prevent or reverse the multidrug resistance of the anticancer drugs. Collectively, (6d) can be considered as a promising lead suitable for further optimization to develop anti-CRC agents or glycoproteins inhibitors.
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30
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Li J, Sun X, Xu J, Tan H, Zeng EY, Chen D. Transplacental Transfer of Environmental Chemicals: Roles of Molecular Descriptors and Placental Transporters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:519-528. [PMID: 33295769 DOI: 10.1021/acs.est.0c06778] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Transplacental transfer of environmental chemicals results in direct risks to fetal development. Although numerous studies have investigated transplacental transfer efficiencies (TTEs) of environmental chemicals, the underlying mechanisms and influencing factors remain poorly understood. The present study aims to synthesize a current state of knowledge on the TTEs of major environmental chemicals and explore the roles of chemicals' molecular descriptors and placental transporters in the transplacental transfer. The results indicate great variations in TTEs (median: 0.29-2.86) across 51 chemicals. Chemical-dependent TTEs may partially be attributed to the influences of chemicals' molecular descriptors. Predictive models based on experimental TTEs and 1790 computed molecular descriptors indicate that a very limited number of molecular descriptors, such as the topological polar surface area, may substantially influence and efficiently predict chemicals' TTEs. In addition, molecular docking analyses were conducted to determine the binding affinities between 51 chemicals and six selected transporters, including BCRP, MDR1, hENT1, FRα, SERT, and MRP1. The results reveal transporter- and chemical-dependent binding affinities. Therefore, our study demonstrates that molecular descriptors and placental transporters, among a variety of other factors, can play important roles in the transplacental transfer of environmental chemicals. However, the underlying mechanisms and several important knowledge gaps identified herein require further investigations.
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Affiliation(s)
- Jing Li
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Xiangfei Sun
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Jun Xu
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Hongli Tan
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Eddy Y Zeng
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Da Chen
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
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31
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Tahmasby M, Darehkordi A, Mohammadi M, Nejadkhorasani F. Pyrido triazin-nucleus synthesis and theoretical studies: 2,3,6-trioxo-8-aryl-1,3,4,6-tetrahydro-]2H[pyrido]1,2-b] [1,2,4[triazin-7,9-dicarbonitryl derivatives. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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32
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Han W, Ding Y, Chen Z, Langowski JL, Bellamacina C, Rico A, Nishiguchi GA, Lan J, Atallah G, Lindvall M, Lin S, Zang R, Feucht P, Zavorotinskaya T, Dai Y, Garcia P, Burger MT. Synthesis and Structure-Activity Relationship of Tetra-Substituted Cyclohexyl Diol Inhibitors of Proviral Insertion of Moloney Virus (PIM) Kinases. J Med Chem 2020; 63:14885-14904. [PMID: 33258605 DOI: 10.1021/acs.jmedchem.0c01279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Overexpression of PIM 1, 2, and 3 kinases is frequently observed in many malignancies. Previously, we discovered a potent and selective pan-PIM kinase inhibitor, compound 2, currently in phase I clinical trials. In this work, we were interested in replacing the amino group on the cyclohexane ring in compound 2 with a hydroxyl group. Structure-based drug design led to cellularly potent but metabolically unstable tetra-substituted cyclohexyl diols. Efforts on the reduction of Log D by introducing polar heterocycles improved metabolic stability. Incorporating fluorine to the tetra-substituted cyclohexyl diol moiety further reduced Log D, resulting in compound 14, a cellularly potent tetra-substituted cyclohexyl diol inhibitor with moderate metabolic stability and good permeability. We also describe the development of efficient and scalable synthetic routes toward synthetically challenging tetra-substituted cyclohexyl diol compounds. In particular, intermediate 36 was identified as a versatile intermediate, enabling a large-scale synthesis of highly substituted cyclohexane derivatives.
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Affiliation(s)
- Wooseok Han
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Yu Ding
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,BeiGene, Ltd., San Mateo, California 94403, United States
| | - Zheng Chen
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,Boston Analytical, Salem, New Hampshire 03079, United States
| | - John L Langowski
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,Kite, a Gilead Company, Emeryville, California 94608, United States
| | - Cornelia Bellamacina
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,Crystallographic Consulting, Berkeley, California 94704, United States
| | - Alice Rico
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,Exelixis, Alameda, California 94502, United States
| | - Gisele A Nishiguchi
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jiong Lan
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,Genfleet Therapeutics, Inc., Pudong District, Shanghai 201203, China
| | - Gordana Atallah
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,Pharmacyclics, an AbbVie Company, Sunnyvale, California 94085, United States
| | - Mika Lindvall
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,Recursion Pharmaceuticals, Salt Lake City, Utah 84101, United States
| | - Song Lin
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,Astex Pharmaceuticals Inc., Pleasanton, California 94588, United States
| | - Richard Zang
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,Global Blood Therapeutics, South San Francisco, California 94080, United States
| | - Paul Feucht
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Tatiana Zavorotinskaya
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,ORIC Pharmaceuticals, South San Francisco, California 94080, United States
| | - Yumin Dai
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,Bristol Myers Squibb, Redwood City, California 94158, United States
| | - Pablo Garcia
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,Circle Pharma, Inc., South San Francisco, California 94080, United States
| | - Matthew T Burger
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.,Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
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33
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Seelig A. P-Glycoprotein: One Mechanism, Many Tasks and the Consequences for Pharmacotherapy of Cancers. Front Oncol 2020; 10:576559. [PMID: 33194688 PMCID: PMC7649427 DOI: 10.3389/fonc.2020.576559] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/31/2020] [Indexed: 12/31/2022] Open
Abstract
P-glycoprotein or multidrug resistance protein (MDR1) is an adenosine triphosphate (ATP) binding cassette transporter (ABCB1) intensely investigated because it is an obstacle to successful pharmacotherapy of cancers. P-glycoprotein prevents cellular uptake of a large number of structurally and functionally diverse compounds, including most cancer therapeutics and in this way causes multidrug resistance (MDR). To overcome MDR, and thus improve cancer treatment, an understanding of P-glycoprotein inhibition at the molecular level is required. With this goal in mind, we propose rules that predict whether a compound is a modulator, substrate, inhibitor, or inducer of P-glycoprotein. This new set of rules is derived from a quantitative analysis of the drug binding and transport properties of P-glycoprotein. We further discuss the role of P-glycoprotein in immune surveillance and cell metabolism. Finally, the predictive power of the proposed rules is demonstrated with a set of FDA approved drugs which have been repurposed for cancer therapy.
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Affiliation(s)
- Anna Seelig
- Biozentrum, University of Basel, Basel, Switzerland
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34
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Lumley JA, Desai P, Wang J, Cahya S, Zhang H. The Derivation of a Matched Molecular Pairs Based ADME/Tox Knowledge Base for Compound Optimization. J Chem Inf Model 2020; 60:4757-4771. [PMID: 32975944 DOI: 10.1021/acs.jcim.0c00583] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Matched Molecular Pairs (MMP) analysis is a well-established technique for Structure Activity and Property Analysis (SAR and SPR). Summarizing multiple MMPs that describe the same structural change into a single chemical transform can be a powerful tool for prediction (termed Transform from here on). This is particularly useful in the area of Absorption, Distribution, Metabolism, and Elimination (ADME) analysis that is less influenced by 3D structural binding effects. The creation of a knowledge database containing many of these Transforms across typical ADME assays promises to be a powerful approach to aid multidimensional optimization. We present a detailed workflow for the derivation of such a database. We include details of an MMP fragmentation algorithm with associated statistical summarization methods for the derivation of Transforms. This is made freely available as part of the LillyMol software package. We describe the application of this method to several ADME/Tox (Toxicity) assay data sets and highlight multiple cases where the impact of traditional medicinal chemistry Transforms is contradicted by MMP data. We also describe the internal software interface used by medicinal chemists to aid the design of new compounds via automated suggestion. This approach utilizes the matched pairs database to "suggest" improved compounds in an automated design scenario. A nonvisual script-based version of the automated suggestions code with an associated set of described chemical Transforms is also made freely available along with this paper and as part of the LillyMol software package. Finally, we contrast this knowledge database against a larger database of all MMPs derived from a 2 million compound diversity set and a subset of MMPs seen in historical discovery projects. The comparison against all transforms in the diversity collection highlights the very low coverage of the transform database as compared to all possible transforms involving 15 atom fragments. The comparison against a smaller subset of Transforms seen on internal Medicinal Chemistry projects shows better coverage of the transform database for a small set of common medicinal chemistry strategies. Within the context of all possible transforms available to a medicinal chemistry project team, the challenge remains to move beyond mere idea generation from past projects toward high quality prediction for novel ADME/Tox modulating Transforms.
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Affiliation(s)
- James A Lumley
- Data Science and Engineering, Lilly Research Laboratories, Eli Lilly and Company, Erl Wood Manor, Windlesham, Surrey GU20 6PH, United Kingdom
| | - Prashant Desai
- Computational ADME, ADME-Toxicology-PKPD, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Jibo Wang
- Discovery Chemistry Research Technologies, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Suntara Cahya
- Discovery Statistics, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, California 92121, United States
| | - Hongzhou Zhang
- Data Science and Engineering, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
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35
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Mollazadeh S, Hadizadeh F, Ferreira RJ. Theoretical studies on 1,4-dihydropyridine derivatives as P-glycoprotein allosteric inhibitors: insights on symmetry and stereochemistry. J Biomol Struct Dyn 2020; 39:4752-4763. [DOI: 10.1080/07391102.2020.1780942] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shirin Mollazadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzin Hadizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ricardo J. Ferreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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36
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Sakai H, Inoue H, Murata K, Toba T, Shimmyo Y, Narii N, Ueno SY, Igawa Y, Takemoto N. Fibroblast growth factor receptor modulators employing diamines with reduced phospholipidosis-inducing potential. Bioorg Med Chem 2020; 28:115562. [PMID: 32616184 DOI: 10.1016/j.bmc.2020.115562] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/01/2020] [Accepted: 05/18/2020] [Indexed: 01/23/2023]
Abstract
SUN13837 (1), a fibroblast growth factor receptor modulator, has been an attractive candidate for treating neurodegenerative diseases. However, one of its metabolites, N-benzyl-4-(methylamino)piperidine (BMP), turned out to possess phospholipidosis-inducing potential (PLIP) in vitro. To obtain SUN13837 analogs with reduced phospholipidosis risk, we replaced BMP with other diamines possessing low PLIP. Our effort led to the discovery of compound 6 with increased efficacy. Further structural modifications to reduce hydrogen bond donors afforded 17 with improved brain exposure. Oral administration of 17 at 1 mg/kg once daily for 10 days showed enhanced recovery of coordinated movement in a rat acute stroke model, suggesting that it is a promising follow-up compound for 1 with reduced risk of phospholipidosis.
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Affiliation(s)
- Hiroki Sakai
- Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
| | - Hidekazu Inoue
- Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kenji Murata
- Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Tetsuya Toba
- Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yoshiari Shimmyo
- Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Nobuhiro Narii
- Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Shin-Ya Ueno
- Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yoshiyuki Igawa
- Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Naohiro Takemoto
- Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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37
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In Silico Prediction of Intestinal Permeability by Hierarchical Support Vector Regression. Int J Mol Sci 2020; 21:ijms21103582. [PMID: 32438630 PMCID: PMC7279352 DOI: 10.3390/ijms21103582] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/14/2020] [Accepted: 05/17/2020] [Indexed: 11/17/2022] Open
Abstract
The vast majority of marketed drugs are orally administrated. As such, drug absorption is one of the important drug metabolism and pharmacokinetics parameters that should be assessed in the process of drug discovery and development. A nonlinear quantitative structure-activity relationship (QSAR) model was constructed in this investigation using the novel machine learning-based hierarchical support vector regression (HSVR) scheme to render the extremely complicated relationships between descriptors and intestinal permeability that can take place through various passive diffusion and carrier-mediated active transport routes. The predictions by HSVR were found to be in good agreement with the observed values for the molecules in the training set (n = 53, r2 = 0.93, q CV 2 = 0.84, RMSE = 0.17, s = 0.08), test set (n = 13, q2 = 0.75-0.89, RMSE = 0.26, s = 0.14), and even outlier set (n = 8, q2 = 0.78-0.92, RMSE = 0.19, s = 0.09). The built HSVR model consistently met the most stringent criteria when subjected to various statistical assessments. A mock test also assured the predictivity of HSVR. Consequently, this HSVR model can be adopted to facilitate drug discovery and development.
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38
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Tinworth CP, Young RJ. Facts, Patterns, and Principles in Drug Discovery: Appraising the Rule of 5 with Measured Physicochemical Data. J Med Chem 2020; 63:10091-10108. [PMID: 32324397 DOI: 10.1021/acs.jmedchem.9b01596] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The rule of 5 was designed to estimate the likelihood of poor absorption or permeation, noting the impact of poor solubility. This Perspective explores the impact of various physicochemical descriptors and contemporary lipophilicity measurements on permeability and solubility, showing that the distribution coefficient log D7.4 (rather than log P) is the most impactful parameter. Molecular weight, almost invariably the defining characteristic of "beyond the rule of 5" compounds, has little impact on solubility when log D7.4 measurements and aromaticity are considered. Predicting permeation is more complex, given passive and carrier transport mechanisms; however, notable patterns of behavior are apparent, giving insight even "beyond the rule of 5". Recommended best practices should involve using the facts (measurements) and the patterns they reveal to establish informative principles rather than fastidious rules.
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Affiliation(s)
- Christopher P Tinworth
- Medicinal Sciences and Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Robert J Young
- Medicinal Sciences and Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.,Blue Burgundy Ltd., Bedford, Bedfordshire MK45 2AD, U.K
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39
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Discovery of Novel Imidazopyridine GSK-3β Inhibitors Supported by Computational Approaches. Molecules 2020; 25:molecules25092163. [PMID: 32380735 PMCID: PMC7248956 DOI: 10.3390/molecules25092163] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 11/17/2022] Open
Abstract
The interest of research groups and pharmaceutical companies to discover novel GSK-3β inhibitors has increased over the years considering the involvement of this enzyme in many pathophysiological processes and diseases. Along this line, we recently reported on 1H-indazole-3-carboxamide (INDZ) derivatives 1-6, showing good GSK-3β inhibition activity. However, they suffered from generally poor central nervous system (CNS) permeability. Here, we describe the design, synthesis, and in vitro characterization of novel imidazo[1,5-a]pyridine-1-carboxamide (IMID 1) and imidazo[1,5-a]pyridine-3-carboxamide (IMID 2) compounds (7-18) to overcome such liability. In detail, structure-based approaches and fine-tuning of physicochemical properties guided the design of derivatives 7-18 resulting in ameliorated absorption, distribution, metabolism, and excretion (ADME) properties. A crystal structure of 16 in complex with GSK-3β enzyme (PDB entry 6Y9S) confirmed the in silico models. Despite the nanomolar inhibition activity, the new core compounds showed a reduction in potency with respect to INDZ derivatives 1-6. In this context, Molecular Dynamics (MD) and Quantum Mechanics (QM) based approaches along with NMR investigation helped to rationalize the observed structure activity relationship (SAR). With these findings, the key role of the acidic hydrogen of the central core for a tight interaction within the ATP pocket of the enzyme reflecting in good GSK-3β affinity was demonstrated.
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Carter DS, Jacobs RT, Freund YR, Berry PW, Akama T, Easom EE, Lunde CS, Rock F, Stefanakis R, McKerrow J, Fischer C, Bulman CA, Lim KC, Suzuki BM, Tricoche N, Sakanari JA, Lustigman S, Plattner JJ. Macrofilaricidal Benzimidazole-Benzoxaborole Hybrids as an Approach to the Treatment of River Blindness: Part 2. Ketone Linked Analogs. ACS Infect Dis 2020; 6:180-185. [PMID: 31876143 PMCID: PMC7026882 DOI: 10.1021/acsinfecdis.9b00397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The optimization
of a series of benzimidazole–benzoxaborole hybrid molecules
linked via a ketone that exhibit good activity against Onchocerca
volvulus, a filarial nematode responsible for the disease
onchocerciasis, also known as river blindness, is described. The lead
identified in this series, 21 (AN15470), was found to
have acceptable pharmacokinetic properties to enable an evaluation
following oral dosing in an animal model of onchocerciasis. Compound 21was effective in killing worms implanted in Mongolian gerbils
when dosed orally as a suspension at 100 mg/kg/day for 14 days but
not when dosed orally at 100 mg/kg/day for 7 days.
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Affiliation(s)
- David S. Carter
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Robert T. Jacobs
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Yvonne R. Freund
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Pamela W. Berry
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Tsutomu Akama
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Eric E. Easom
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Christopher S. Lunde
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Fernando Rock
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Rianna Stefanakis
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - James McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0657, United States
| | - Chelsea Fischer
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, California 94158, United States
| | - Christina A. Bulman
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, California 94158, United States
| | - Kee Chong Lim
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, California 94158, United States
| | - Brian M. Suzuki
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0657, United States
| | - Nancy Tricoche
- Lindsley F. Kimball Research Institute, New York Blood Center, 310 E. 67th Street, New York, New York 10065, United States
| | - Judy A. Sakanari
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, California 94158, United States
| | - Sara Lustigman
- Lindsley F. Kimball Research Institute, New York Blood Center, 310 E. 67th Street, New York, New York 10065, United States
| | - Jacob J. Plattner
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
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41
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Akama T, Freund YR, Berry PW, Carter DS, Easom EE, Jarnagin K, Lunde CS, Plattner JJ, Rock F, Stefanakis R, Fischer C, Bulman CA, Lim KC, Suzuki BM, Tricoche N, Mansour A, DiCosty U, McCall S, Carson B, McCall JW, McKerrow J, Hübner MP, Specht S, Hoerauf A, Lustigman S, Sakanari JA, Jacobs RT. Macrofilaricidal Benzimidazole-Benzoxaborole Hybrids as an Approach to the Treatment of River Blindness: Part 1. Amide Linked Analogs. ACS Infect Dis 2020; 6:173-179. [PMID: 31876154 PMCID: PMC7026885 DOI: 10.1021/acsinfecdis.9b00396] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A series of benzimidazole–benzoxaborole
hybrid molecules
linked via an amide linker are described that exhibit good in vitro activity against Onchocerca volvulus, a filarial nematode responsible for the disease onchocerciasis,
also known as river blindness. The lead identified in this series, 8a (AN8799), was found to have acceptable pharmacokinetic
properties to enable evaluation in animal models of human filariasis.
Compound 8a was effective in killing Brugia malayi, B. pahangi, and Litomosoides sigmodontis worms present in Mongolian gerbils when dosed subcutaneously as
a suspension at 100 mg/kg/day for 14 days but not when dosed orally
at 100 mg/kg/day for 28 days. The measurement of plasma levels of 8a at the end of the dosing period and at the time of sacrifice
revealed an interesting dependence of activity on the extended exposure
for both 8a and the positive control, flubendazole.
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Affiliation(s)
- Tsutomu Akama
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Yvonne R. Freund
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Pamela W. Berry
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - David S. Carter
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Eric E. Easom
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Kurt Jarnagin
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Christopher S. Lunde
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Jacob J. Plattner
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Fernando Rock
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Rianna Stefanakis
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
| | - Chelsea Fischer
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, California 94158, United States
| | - Christina A. Bulman
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, California 94158, United States
| | - Kee Chong Lim
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, California 94158, United States
| | - Brian M. Suzuki
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0657, United States
| | - Nancy Tricoche
- Lindsley F. Kimball Research Institute, New York Blood Center, 310 E. 67th Street, New York, New York 10065, United States
| | - Abdelmoneim Mansour
- TRS Laboratories, Inc., 295 Research Drive, Athens, Georgia 30605, United States
| | - Utami DiCosty
- TRS Laboratories, Inc., 295 Research Drive, Athens, Georgia 30605, United States
| | - Scott McCall
- TRS Laboratories, Inc., 295 Research Drive, Athens, Georgia 30605, United States
| | - Ben Carson
- TRS Laboratories, Inc., 295 Research Drive, Athens, Georgia 30605, United States
| | - John W. McCall
- TRS Laboratories, Inc., 295 Research Drive, Athens, Georgia 30605, United States
| | - James McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0657, United States
| | - Marc P. Hübner
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Sigmund Freud Strasse 25, 53127 Bonn, Germany
| | - Sabine Specht
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Sigmund Freud Strasse 25, 53127 Bonn, Germany
- Drugs for Neglected Diseases Initiative, 15 Chemin Louis-Dunant, 1202 Geneva, Switzerland
| | - Achim Hoerauf
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Sigmund Freud Strasse 25, 53127 Bonn, Germany
| | - Sara Lustigman
- Lindsley F. Kimball Research Institute, New York Blood Center, 310 E. 67th Street, New York, New York 10065, United States
| | - Judy A. Sakanari
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, California 94158, United States
| | - Robert T. Jacobs
- Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, California 94303, United States
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Amaradhi R, Banik A, Mohammed S, Patro V, Rojas A, Wang W, Motati DR, Dingledine R, Ganesh T. Potent, Selective, Water Soluble, Brain-Permeable EP2 Receptor Antagonist for Use in Central Nervous System Disease Models. J Med Chem 2020; 63:1032-1050. [PMID: 31904232 PMCID: PMC7394479 DOI: 10.1021/acs.jmedchem.9b01218] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Activation of prostanoid EP2 receptor exacerbates neuroinflammatory and neurodegenerative pathology in central nervous system diseases such as epilepsy, Alzheimer's disease, and cerebral aneurysms. A selective and brain-permeable EP2 antagonist will be useful to attenuate the inflammatory consequences of EP2 activation and to reduce the severity of these chronic diseases. We recently developed a brain-permeable EP2 antagonist 1 (TG6-10-1), which displayed anti-inflammatory and neuroprotective actions in rodent models of status epilepticus. However, this compound exhibited moderate selectivity to EP2, a short plasma half-life in rodents (1.7 h) and low aqueous solubility (27 μM), limiting its use in animal models of chronic disease. With lead-optimization studies, we have developed several novel EP2 antagonists with improved water solubility, brain penetration, high EP2 potency, and selectivity. These novel inhibitors suppress inflammatory gene expression induced by EP2 receptor activation in a microglial cell line, reinforcing the use of EP2 antagonists as anti-inflammatory agents.
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Affiliation(s)
- Radhika Amaradhi
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Rd; Atlanta, GA, 30322, United States of America
| | - Avijit Banik
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Rd; Atlanta, GA, 30322, United States of America
| | - Shabber Mohammed
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Rd; Atlanta, GA, 30322, United States of America
| | - Vidyavathi Patro
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Rd; Atlanta, GA, 30322, United States of America
| | - Asheebo Rojas
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Rd; Atlanta, GA, 30322, United States of America
| | - Wenyi Wang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Rd; Atlanta, GA, 30322, United States of America
| | - Damoder Reddy Motati
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Rd; Atlanta, GA, 30322, United States of America
| | - Ray Dingledine
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Rd; Atlanta, GA, 30322, United States of America
| | - Thota Ganesh
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Rd; Atlanta, GA, 30322, United States of America
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43
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Yang ZY, He JH, Lu AP, Hou TJ, Cao DS. Application of Negative Design To Design a More Desirable Virtual Screening Library. J Med Chem 2020; 63:4411-4429. [DOI: 10.1021/acs.jmedchem.9b01476] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Zi-Yi Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Jun-Hong He
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Ai-Ping Lu
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, P. R. China
| | - Ting-Jun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dong-Sheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, P. R. China
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44
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Yang H, Li H, Zhou M, Wei T, Tang C, Liu L, Zhou Y, Long X. A relationship between membrane permeation and partitioning of nitroaromatic explosives and their functional groups. A computational study. Phys Chem Chem Phys 2020; 22:8791-8799. [DOI: 10.1039/d0cp00549e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nitroaromatic explosives, such as 2,4,6-trinitrotoluene, are representative aromatic compounds, which are generally highly toxic.
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Affiliation(s)
- Hong Yang
- School of Materials Science and Engineering
- Tsinghua University
- Beijing 100084
- China
- Institute of Chemical Materials
| | - Huarong Li
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
| | - Mi Zhou
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
| | - Tong Wei
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
| | - Can Tang
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
| | - Liu Liu
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
| | - Yang Zhou
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
| | - Xinping Long
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
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45
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Dually Acting Nonclassical 1,4-Dihydropyridines Promote the Anti-Tuberculosis (Tb) Activities of Clofazimine. Molecules 2019; 24:molecules24162873. [PMID: 31398786 PMCID: PMC6720424 DOI: 10.3390/molecules24162873] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/26/2019] [Accepted: 08/01/2019] [Indexed: 11/17/2022] Open
Abstract
The number of effective antituberculotic drugs is strongly limited to four first-line drugs in standard therapy. In case of resistances second-line antibiotics are used with a poor efficacy and tolerability. Therefore, novel antituberculotic drugs are urgently needed. We synthesized novel nonclassical 1,4-dihydropyridines and evaluated their antituberculotic properties depending on substituent effects. Preferred substituents could be identified. As related classical 1,4-dihydropyridines are known as inhibitors of the transmembrane efflux pump ABCB1 in cancer cells, we wondered whether a use of our compounds may be of favour to enhance the antituberculotic drug efficacy of the second-line antituberculotic drug clofazimine, which is a known substrate of ABCB1 by a suggested inhibition of a corresponding efflux pump in Mycobacterium tuberculosis (Mtb). For this, we determined the ABCB1 inhibiting properties of our compounds in a mouse T-lymphoma cell line model and then evaluated the drug-enhancing properties of selected compounds in a co-application with clofazimine in our Mtb strain. We identified novel enhancers of clofazimine toxicity which could prevent clofazimine resistance development mediated by an efflux pump activity.
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46
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Shamsimeymandi R, Pourshojaei Y, Eskandari K, Mohammadi-Khanaposhtani M, Abiri A, Khodadadi A, Langarizadeh A, Sharififar F, Amirheidari B, Akbarzadeh T, Lotfian H, Foroumadi A, Asadipour A. Design, synthesis, biological evaluation, and molecular dynamics of novel cholinesterase inhibitors as anti-Alzheimer's agents. Arch Pharm (Weinheim) 2019; 352:e1800352. [PMID: 31136018 DOI: 10.1002/ardp.201800352] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/09/2019] [Accepted: 04/12/2019] [Indexed: 11/08/2022]
Abstract
A series of novel chroman-4-one derivatives were designed and synthesized successfully with good to excellent yield (3a-l). In addition, the obtained products were evaluated for their cholinesterase (ChE) inhibitory activities. The results show that among the various synthesized compounds, analogs bearing the piperidinyl ethoxy side chain with 4-hydroxybenzylidene on the 3-positions of chroman-4-one (3l) showed the most potent activity with respect to acetylcholinesterase (anti-AChE activity; IC50 = 1.18 μM). In addition, the structure-activity relationship was studied and the results revealed that the electron-donating groups on the aryl ring of the 3-benzylidene fragment (3k, 3l) resulted in the designed compounds to be more potent ChE inhibitors in comparison with those having electron-withdrawing groups (3h). In this category, the strongest ChE inhibition was found for the compound containing piperidine as cyclic amine, and a hydroxyl group (for AChE, compound 3l) and fluoro group (for butyrylcholinesterase (BuChE, compound 3i) on the para-position of the aryl ring of the benzylidene group. The molecular docking and dynamics studies of the most potent compounds (3i and 3l against BuChE and AChE, respectively) demonstrated remarkable interactions with the binding pockets of the ChE enzymes and confirmed the results obtained through in vitro experiments.
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Affiliation(s)
- Reza Shamsimeymandi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Yaghoub Pourshojaei
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran.,Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Khalil Eskandari
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Maryam Mohammadi-Khanaposhtani
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Arash Khodadadi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Fariba Sharififar
- Department of Pharmacognosy, School of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Bagher Amirheidari
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Tahmineh Akbarzadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.,Persian Medicine and Pharmacy Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hania Lotfian
- Persian Medicine and Pharmacy Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Foroumadi
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran.,Drug Design and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Asadipour
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
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Fushimi M, Fujimori I, Wakabayashi T, Hasui T, Kawakita Y, Imamura K, Kato T, Murakami M, Ishii T, Kikko Y, Kasahara M, Nakatani A, Hiura Y, Miyamoto M, Saikatendu K, Zou H, Lane SW, Lawson JD, Imoto H. Discovery of Potent, Selective, and Brain-Penetrant 1H-Pyrazol-5-yl-1H-pyrrolo[2,3-b]pyridines as Anaplastic Lymphoma Kinase (ALK) Inhibitors. J Med Chem 2019; 62:4915-4935. [DOI: 10.1021/acs.jmedchem.8b01630] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Makoto Fushimi
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Ikuo Fujimori
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takeshi Wakabayashi
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tomoaki Hasui
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Youichi Kawakita
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Keisuke Imamura
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tomoko Kato
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Morio Murakami
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tsuyoshi Ishii
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yorifumi Kikko
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Maki Kasahara
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Atsushi Nakatani
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yuto Hiura
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Maki Miyamoto
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kumar Saikatendu
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - Hua Zou
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - Scott Weston Lane
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - J. David Lawson
- Takeda California, Inc., 10410 Science Center Drive, San Diego, California 92121, United States
| | - Hiroshi Imoto
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
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48
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High-throughput hydrogen bond strength calculation and its applications in optimizing drug ADME properties. Future Med Chem 2019; 11:511-524. [PMID: 30892942 DOI: 10.4155/fmc-2018-0470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
AIM Modifying the molecule's intrinsic hydrogen bond strength (HBS) is a useful approach in optimizing its permeability and P-glycoprotein (P-gp) efflux. Quantum mechanics (QM) based computation has been utilized to estimate the molecular intrinsic HBS. Despite its usefulness, the computation is time consuming for a large set of molecules. METHODOLOGY/RESULTS We introduced a fragment-based high-throughput HBS calculation method and validated it with internal and external datasets. Examples have been presented where the P-gp efflux and permeability can be optimized by modulating calculated HBS. CONCLUSION The results will enable medicinal chemists to calculate HBS in a high-throughput manner while optimizing permeability and P-gp efflux. This will further improve the efficiency of balancing multiple properties during drug discovery process.
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49
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Chen D, Zhao M, Tan W, Li Y, Li X, Li Y, Fan X. Effects of intramolecular hydrogen bonds on lipophilicity. Eur J Pharm Sci 2019; 130:100-106. [DOI: 10.1016/j.ejps.2019.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/08/2019] [Accepted: 01/18/2019] [Indexed: 12/22/2022]
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50
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Attram HD, Wittlin S, Chibale K. Incorporation of an intramolecular hydrogen bonding motif in the side chain of antimalarial benzimidazoles. MEDCHEMCOMM 2019; 10:450-455. [PMID: 31015908 DOI: 10.1039/c8md00608c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/14/2019] [Indexed: 11/21/2022]
Abstract
Analogues of a novel class of benzimidazoles with an intramolecular hydrogen bonding motif have been synthesized and evaluated in vitro for their antiplasmodium activity against chloroquine-sensitive (NF54) and multi-drug resistant (K1) strains of the human malaria parasite Plasmodium falciparum. Compounds were also screened for their cytotoxicity towards a mammalian Chinese hamster ovarian (CHO) cell line. Most of the compounds exhibited good antiplasmodium activity (PfNF54 IC50 <1 μM) and were relatively noncytotoxic. Moreover, towards establishing the possible mode of action of these molecules, inhibition of beta-hematin formation was investigated and two compounds were found to be inhibitors. Single crystal X-ray data confirmed the existence of an intramolecular hydrogen bond.
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Affiliation(s)
- Henrietta D Attram
- Department of Chemistry , University of Cape Town , Rondebosch 7701 , South Africa . ; ; Tel: +27 21 6502553
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute , Socinstrasse 57 , 4002 Basel , Switzerland.,University of Basel , 4003 Basel , Switzerland
| | - Kelly Chibale
- Department of Chemistry , University of Cape Town , Rondebosch 7701 , South Africa . ; ; Tel: +27 21 6502553.,South African Medical Research Council Drug Discovery and Development Research Unit , Department of Chemistry , University of Cape Town , Rondebosch 7701 , South Africa.,Institute of Infectious Disease and Molecular Medicine , University of Cape Town , Rondebosch 7701 , South Africa
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