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Pasamba EC, Orda MA, Villanueva BHA, Tsai PW, Tayo LL. Transcriptomic Analysis of Hub Genes Reveals Associated Inflammatory Pathways in Estrogen-Dependent Gynecological Diseases. BIOLOGY 2024; 13:397. [PMID: 38927277 PMCID: PMC11201105 DOI: 10.3390/biology13060397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Gynecological diseases are triggered by aberrant molecular pathways that alter gene expression, hormonal balance, and cellular signaling pathways, which may lead to long-term physiological consequences. This study was able to identify highly preserved modules and key hub genes that are mainly associated with gynecological diseases, represented by endometriosis (EM), ovarian cancer (OC), cervical cancer (CC), and endometrial cancer (EC), through the weighted gene co-expression network analysis (WGCNA) of microarray datasets sourced from the Gene Expression Omnibus (GEO) database. Five highly preserved modules were observed across the EM (GSE51981), OC (GSE63885), CC (GSE63514), and EC (GSE17025) datasets. The functional annotation and pathway enrichment analysis revealed that the highly preserved modules were heavily involved in several inflammatory pathways that are associated with transcription dysregulation, such as NF-kB signaling, JAK-STAT signaling, MAPK-ERK signaling, and mTOR signaling pathways. Furthermore, the results also include pathways that are relevant in gynecological disease prognosis through viral infections. Mutations in the ESR1 gene that encodes for ERα, which were shown to also affect signaling pathways involved in inflammation, further indicate its importance in gynecological disease prognosis. Potential drugs were screened through the Drug Repurposing Encyclopedia (DRE) based on the up-and downregulated hub genes, wherein a bacterial ribosomal subunit inhibitor and a benzodiazepine receptor agonist were the top candidates. Other drug candidates include a dihydrofolate reductase inhibitor, glucocorticoid receptor agonists, cholinergic receptor agonists, selective serotonin reuptake inhibitors, sterol demethylase inhibitors, a bacterial antifolate, and serotonin receptor antagonist drugs which have known anti-inflammatory effects, demonstrating that the gene network highlights specific inflammatory pathways as a therapeutic avenue in designing drug candidates for gynecological diseases.
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Affiliation(s)
- Elaine C. Pasamba
- School of Graduate Studies, Mapúa University, Manila City 1002, Philippines; (E.C.P.); (M.A.O.); (B.H.A.V.)
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila City 1002, Philippines
| | - Marco A. Orda
- School of Graduate Studies, Mapúa University, Manila City 1002, Philippines; (E.C.P.); (M.A.O.); (B.H.A.V.)
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila City 1002, Philippines
| | - Brian Harvey Avanceña Villanueva
- School of Graduate Studies, Mapúa University, Manila City 1002, Philippines; (E.C.P.); (M.A.O.); (B.H.A.V.)
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila City 1002, Philippines
| | - Po-Wei Tsai
- Department of Food Science, National Taiwan Ocean University, Keelung 20224, Taiwan;
| | - Lemmuel L. Tayo
- School of Graduate Studies, Mapúa University, Manila City 1002, Philippines; (E.C.P.); (M.A.O.); (B.H.A.V.)
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila City 1002, Philippines
- Department of Biology, School of Health Sciences, Mapúa University, Makati City 1203, Philippines
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2
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Zhu Z, Chen C, Zhang J, Lai F, Feng J, Wu G, Xia J, Zhang W, Han Z, Zhang C, Yang Q, Wang Y, Liu B, Li T, Wu S. Exploration and Biological Evaluation of 1,3-Diamino-7 H-pyrrol[3,2- f]quinazoline Derivatives as Dihydrofolate Reductase Inhibitors. J Med Chem 2023; 66:13946-13967. [PMID: 37698518 DOI: 10.1021/acs.jmedchem.3c00891] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Dihydrofolate reductase (DHFR), a core enzyme of folate metabolism, plays a crucial role in the biosynthesis of purines and thymidylate for cell proliferation and growth in both prokaryotic and eukaryotic cells. However, the development of new DHFR inhibitors is challenging due to the limited number of scaffolds available for drug development. Hence, we designed and synthesized a new class of DHFR inhibitors with a 1,3-diamino-7H-pyrrol[3,2-f]quinazoline derivative (PQD) structure bearing condensed rings. Compound 6r exhibited therapeutic effects on mouse models of systemic infection and thigh infection caused by methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43300. Moreover, methyl-modified PQD compound 8a showed a strong efficacy in a murine model of breast cancer, which was better than the effects of taxol. The findings showcased in this study highlight the promising capabilities of novel DHFR inhibitors in addressing bacterial infections as well as breast cancer.
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Affiliation(s)
- Zihao Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Cantong Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jie Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Fangfang Lai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jing Feng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guangxu Wu
- Department of Pharmacy, The People Hospital of Liupanshui City, Guizhou, Liupanshui 553000, China
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wenxuan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zunsheng Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Chi Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Qingyun Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yuchen Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Bo Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Tianlei Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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3
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Dawood DH, Sayed MM, Tohamy STK, Nossier ES. New Thiophenyl-pyrazolyl-thiazole Hybrids as DHFR Inhibitors: Design, Synthesis, Antimicrobial Evaluation, Molecular Modeling, and Biodistribution Studies. ACS OMEGA 2023; 8:39250-39268. [PMID: 37901585 PMCID: PMC10600881 DOI: 10.1021/acsomega.3c04736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023]
Abstract
The antibiotic resistance problems constitute a considerable threat to human health worldwide; thus, the discovery of new antimicrobial candidates to conquer this issue is an imperative requirement. From this view, new thiophenyl-pyrazolyl-thiazole hybrids 3-10 were synthesized and screened for their antibacterial efficiency versus Gram - and Gram + bacterial strains compared to the reference drug amoxicillin. It was noticed that the new hybrids displayed significant antibacterial efficacy versus Gram - bacteria, especially against Pseudomonas aeruginosa. Also, all the screened candidates demonstrated a noticeable antifungal effect against Candida albicans (MICs = 3.9-125 μg/mL) relative to fluconazole (MIC = 250 μg/mL). Moreover, the new hybrids were investigated for their antituberculosis potency against Mycobacterium tuberculosis (RCMB 010126). Derivatives 4c, 6b, 8b, 9b, and 10b demonstrated prominent antituberculosis efficiency (MICs = 0.12-1.95 μg/mL) compared with the reference drug isoniazid (MIC = 0.12 μg/mL). The latter derivatives were further assessed for their inhibitory potency versus M. tuberculosis DHFR enzyme. The compounds 4c, 6b and 10b presented a remarkable suppression effect with IC50 values of 4.21, 5.70, and 10.59 μM, respectively, compared to that of trimethoprim (IC50 = 6.23 μM). Furthermore, biodistribution profile using radiolabeling way revealed a perceived uptake of 131I-compound 6b into infection induced models. The docking study for the new hybrids 4c, 6b, 8b, 9b and 10b was performed to illustrate the various binding modes with Mtb DHFR enzyme. In silico ADMET studies for the most potent inhibitors 4c, 6b and 10b were also accomplished to predict their pharmacokinetic and physicochemical features.
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Affiliation(s)
- Dina H. Dawood
- Chemistry
of Natural and Microbial Products Department, Pharmaceutical and Drug
Industries Research Institute, National
Research Centre, 33 El
Bohouth Street, Dokki, Giza 12622, Egypt
| | - Manal M. Sayed
- Labeled
Compounds Department, Hot Labs.center, Egyptian
Atomic Energy Authority (EAEA), P.O.
Box 13759, Cairo, Egypt
| | - Sally T. K. Tohamy
- Department
of Microbiology and Immunology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11754, Egypt
| | - Eman S. Nossier
- Department
of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of
Pharmacy (Girls), Al-Azhar University, Cairo 11754, Egypt
- The
National Committee of Drugs, Academy of
Scientific Research and Technology, Cairo 11516, Egypt
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4
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Gurushankar K, Rimac H, Nadezhda P, Grishina M. Exploring the potential and identifying Withania somnifera alkaloids as novel dihydrofolate reductase (DHFR) inhibitors by the AlteQ method. J Biomol Struct Dyn 2023; 41:13963-13976. [PMID: 36762693 DOI: 10.1080/07391102.2023.2175727] [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: 10/07/2022] [Accepted: 01/29/2023] [Indexed: 02/11/2023]
Abstract
There is an urgent need to discover and develop novel drugs to combat Mycobacterium tuberculosis, the causative agent of tuberculosis (TB) in humans. Alkaloids have been shown to have wide-ranging therapeutic application and could be ideal candidates for drug development, and research is underway to develop new anti-tubercular drugs from natural sources. In this regard, the current research deals with finding novel lead compounds from the Withania somnifera (WS) plant. Broad health benefits of WS are due to the presence of diverse chemical constituents which include anaferine and anahygrine and which belong to the alkaloid family. In the present study, these two compounds have been theoretically studied to understand their electronic properties using the density functional theory (DFT) at the B3LYP/6-311 + G (d,p) level. HOMO and LUMO properties and molecular electrostatic potential (MEP) surface were calculated. Further, to understand the mechanism of action of these compounds and to identify their putative drug target, molecular docking and dynamics studies were employed against Mycobacterium tuberculosis dihydrofolate reductase (DHFR). It was determined that NADP+ affects stability of the complexes by reducing fluctuations of residues 14-23 and 117-126. It was also found that Ile5 and Gln28 play an important role in complexation. Electron density analysis (using the AlteQ method) of the intermolecular region, analyzing both the anaferin-NADP+ and anahygrin-NADP+ complexes showed that anaferin and anahygrin complexes are more stable in the presence of NADP+. It has been established that in most intermolecular contacts the contribution of the ligand to the electron density is greater than that of NADP+. The present study thus provides an excellent way to analyze the effect of anaferine and anahygrine in essential processes of M. tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Krishnamoorthy Gurushankar
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
- Department of Physics, Kalasalingam Academy of Research and Education, Krishnankoil, Tamilnadu, India
| | - Hrvoje Rimac
- Department of Medicinal Chemistry, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Palko Nadezhda
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
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5
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Kushwaha N, Sahu A, Mishra J, Soni A, Dorwal D. An Insight on the Prospect of Quinazoline and Quinazolinone Derivatives as Anti-tubercular Agents. Curr Org Synth 2023; 20:838-869. [PMID: 36927421 DOI: 10.2174/1570179420666230316094435] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 01/22/2023] [Accepted: 01/27/2023] [Indexed: 03/18/2023]
Abstract
Multiple potential drugs have been developed based on the heterocyclic molecules for the treatment of different symptoms. Among the existing heterocyclic molecules, quinazoline and quinazolinone derivatives have been found to exhibit extensive pharmacological and biological characteristics. One significant property of these molecules is their potency as anti-tubercular agents. Thus, both quinazoline and quinazolinone derivatives are modified using different functional groups as substituents for investigating their anti-tubercular activities. We present a summary of the reported anti-tubercular drugs, designed using quinazoline and quinazolinone derivatives, in this review.
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Affiliation(s)
| | - Adarsh Sahu
- Department of Pharmaceutical Sciences, Harisingh Gour Vishwavidyalaya, Sagar, MP, India
| | - Jyotika Mishra
- Department of Pharmaceutical Sciences, Harisingh Gour Vishwavidyalaya, Sagar, MP, India
| | - Ankit Soni
- Sri Aurobindo Institute of Pharmacy, Indore, MP, India
| | - Dhawal Dorwal
- Sri Aurobindo Institute of Pharmacy, Indore, MP, India
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6
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The Anti-Multidrug-Resistant Acinetobacter baumannii Study on 1,3-diamino-7H-pyrrolo[3,2-f]quinazoline Compounds. Molecules 2022; 27:molecules27238609. [PMID: 36500701 PMCID: PMC9735644 DOI: 10.3390/molecules27238609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
As a major public health problem, the prevalence of Acinetobacter baumannii (A. baumannii) infections in hospitals due to the pathogen's multiple-antibiotic resistance has attracted extensive attention. We previously reported a series of 1,3-diamino-7H-pyrrolo[3,2-f]quinazoline (PQZ) compounds, which were designed by targeting Escherichia coli dihydrofolate reductase (ecDHFR), and exhibited potent antibacterial activities. In the current study, based on our molecular-modeling study, it was proposed that PQZ compounds may function as potent A. baumannii DHFR (abDHFR)-inhibitors as well, which inspired us to consider their anti-A. baumannii abilities. We further found that three PQZ compounds, OYYF-171, -172, and -175, showed significant antibacterial activities against A. baumannii, including multidrug-resistant (MDR) strains, which are significantly stronger than the typical DHFR-inhibitor, trimethoprim (TMP), and superior to, or comparable to, the other tested antibacterial agents belonging to β-lactam, aminoglycoside, and quinolone. The significant synergistic effect between the representative compound OYYF-171 and the dihydropteroate synthase (DHPS)-inhibitor sulfamethoxazole (SMZ) was observed in both the microdilution-checkerboard assay and time-killing assay, which indicated that using SMZ in combination with PQZ compounds could help to reduce the required dosage and forestall resistance. Our study shows that PQZ is a promising scaffold for the further development of folate-metabolism inhibitors against MDR A. baumannii.
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7
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He J, Li C, Hu W, Li C, Liu S, Sui J, Zhang T, Sun Q, Luo Y. Identification of selective mtbDHFR inhibitors by virtual screening and experimental approaches. Chem Biol Drug Des 2022; 100:1005-1016. [PMID: 34981654 DOI: 10.1111/cbdd.14018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/26/2021] [Accepted: 12/18/2021] [Indexed: 02/05/2023]
Abstract
mtbDHFR-targeting inhibition has become a promising approach for tuberculosis treatment. In the current research, a multi-step virtual screening effort toward ZINC and MCE databases was devoted to discover novel mtbDHFR inhibitors. Based on binding affinity of small molecules through molecular docking study in AutoDock Vina, the number of compounds was reduced to 952,688. Further, these compounds were employed by a step-by-step multiple docking programs of Schrödinger suite and filtered by pharmacokinetics and PAINS parameters. Finally, nine ZINC compounds and 400 MCE compounds were obtained. These compounds of binding ability were tested with mtbDHFR by FluoPol-ABPP approach established in this work. Finally, AF-353 compound was found to have strong binding effect to mtbDHFR. AF-353 was further tested for mtb and hDHFR enzymatic activities, and it was proved to possess 50-fold selectivity toward mtbDHFR over hDHFR. In silico MD simulation results supported this selectivity.
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Affiliation(s)
- Juan He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Cong Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Wei Hu
- Chengdu FenDi pharmaceutical Co., Ltd., Chengdu, China
| | - Chungen Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Song Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Jing Sui
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Qingxiang Sun
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
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Jiang X, Lin Y, Wu Y, Yuan C, Lang X, Chen J, Zhu C, Yang X, Huang Y, Wang H, Wu C. Identification of potential anti-pneumonia pharmacological components of Glycyrrhizae Radix et Rhizoma after the treatment with Gan An He Ji oral liquid. J Pharm Anal 2022; 12:839-851. [PMID: 36605579 PMCID: PMC9805948 DOI: 10.1016/j.jpha.2022.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 01/07/2023] Open
Abstract
Glycyrrhizae Radix et Rhizoma, a traditional Chinese medicine also known as Gan Cao (GC), is frequently included in clinical prescriptions for the treatment of pneumonia. However, the pharmacological components of GC for pneumonia treatment are rarely explored. Gan An He Ji oral liquid (GAHJ) has a simple composition and contains GC liquid extracts and paregoric, and has been used clinically for many years. Therefore, GAHJ was selected as a compound preparation for the study of GC in the treatment of pneumonia. We conducted an in vivo study of patients with pneumonia undergoing GAHJ treatments for three days. Using the intelligent mass spectrometry data-processing technologies to analyze the metabolism of GC in vivo, we obtained 168 related components of GC in humans, consisting of 24 prototype components and 144 metabolites, with 135 compounds screened in plasma and 82 in urine. After analysis of the metabolic transformation relationship and relative exposure, six components (liquiritin, liquiritigenin, glycyrrhizin, glycyrrhetinic acid, daidzin, and formononetin) were selected as potential effective components. The experimental results based on two animal pneumonia models and the inflammatory cell model showed that the mixture of these six components was effective in the treatment of pneumonia and lung injury and could effectively downregulate the level of inducible nitric oxide synthase (iNOS). Interestingly, glycyrrhetinic acid exhibited the strongest inhibition on iNOS and the highest exposure in vivo. The following molecular dynamic simulations indicated a strong bond between glycyrrhetinic acid and iNOS. Thus, the current study provides a pharmaceutical basis for GC and reveals the possible corresponding mechanisms in pneumonia treatment.
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Affiliation(s)
- Xiaojuan Jiang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cell Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yihua Lin
- Department of Respiratory and Critical Care Medicine, The Third Clinical Medical College, Fujian Medical University, Fuzhou, 350122, China,Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Yunlong Wu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cell Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Caixia Yuan
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cell Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xuli Lang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cell Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jiayun Chen
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cell Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Chunyan Zhu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cell Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xinyi Yang
- Laboratory of Pharmacology/Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yu Huang
- School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Hao Wang
- School of Pharmacy, Minzu University of China, Beijing, 100081, China,Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, 100081, China,Institute of National Security, Minzu University of China, Beijing, 100081, China,Corresponding author. School of Pharmacy, Minzu University of China, Beijing, 100081, China.
| | - Caisheng Wu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cell Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, 361102, China,Corresponding author.
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9
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Bhagat K, Kumar N, Kaur Gulati H, Sharma A, Kaur A, Singh JV, Singh H, Bedi PMS. Dihydrofolate reductase inhibitors: patent landscape and phases of clinical development (2001-2021). Expert Opin Ther Pat 2022; 32:1079-1095. [PMID: 36189616 DOI: 10.1080/13543776.2022.2130752] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Dihydrofolate reductase (DHFR) plays an important role in the biosynthesis of amino acid and folic acid. It participates by reducing dihydrofolate to tetrahydrofolate, in the presence of nicotinamide dinucleotide phosphate cofactor, and has been verified by various clinical studies to use DHFR as a target for the treatment of cancer and various bacterial infections. AREA COVERED In this review, we have disclosed patents of synthetics and natural DHFR inhibitors with diaminopyrimidine and quinazoline nucleus from 2001. Additionally, this review highlights the clinical progression of numerous DHFR inhibitors received from the last five years. EXPERT OPINION From 2001 to 2021, numerous active chemical scaffolds have been introduced and are exposed as lead candidates that have entered clinical trials as potent DHFR inhibitors. Moreover, researchers have paid considerable attention to the development of a new class of DHFR inhibitors with higher selectivity and potency. This development includes synthesis of synthetic as well as natural compounds that are potent DHFR inhibitors. On the basis of literature review, we can anticipate that there are a huge number of novel active molecules available for the future that could possess superior abilities to target this enzyme with a profound pharmacological profile.
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Affiliation(s)
- Kavita Bhagat
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India.,Department of Pharmaceutical Sciences, Khalsa College of Pharmacy, Amritsar, India
| | - Nitish Kumar
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
| | | | - Aanchal Sharma
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
| | - Amandeep Kaur
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
| | - Jatinder Vir Singh
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
| | - Harbinder Singh
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
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10
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Joshi T, Sharma P, Joshi T, Mathpal S, Pande V, Chandra S. Repurposing of FDA approved drugs against Salmonella enteric serovar Typhi by targeting dihydrofolate reductase: an in silico study. J Biomol Struct Dyn 2022; 40:3731-3744. [PMID: 33251976 DOI: 10.1080/07391102.2020.1850356] [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: 07/30/2020] [Accepted: 11/08/2020] [Indexed: 10/22/2022]
Abstract
Drug-resistant Salmonella enteric serovar Typhi (S. Typhi) poses a vital public health issue. To overcome drug resistance issues, the development of effective drugs with novel mechanism(s) of action is required. In this regard, drug repurposing is a viable alternative approach to find novel drugs to overcome drug resistance. Therefore, a FDA-approved-drug-library containing 1930 drugs was analyzed against the dihydrofolate reductase (DHFR) of S. Typhi using deep learning regression algorithms. Initially, a total of 500 compounds were screened, followed by rescreening by molecular docking. Further, from screened compounds by molecular docking, the top eight compounds were subjected to molecular dynamics (MD) simulation. Analysis of MD simulation resulted in four potential compounds, namely; Duvelisib, Amenamevir, Lifitegrast and Nilotinib against the DHFR enzyme. During the MD simulation, these four drugs achieved good stability during the 100 ns trajectory period at 300 K. Further to know the insights of the complex's stability, we calculated RMSF, RG, SASA and interaction energy for the last 60 ns trajectory period because all complexes showed the stability after 40 ns trajectory period. MM-PBSA analysis of the last 10 ns of MD trajectories showed the stability of the complexes. From our results, we conclude that these drugs can also be useful for treating typhoid fever and can inhibit S. Typhi by interfering with the function of the DHFR enzyme. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tushar Joshi
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Bhimtal, Uttarakhand, India
| | - Priyanka Sharma
- Department of Botany, Kumaun University, DSB Campus, Nainital, Uttarakhand, India
| | - Tanuja Joshi
- Computational Biology & Biotechnology Laboratory, Department of Botany, Kumaun University, SSJ Campus, Almora, Uttarakhand, India
| | - Shalini Mathpal
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Bhimtal, Uttarakhand, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Bhimtal, Uttarakhand, India
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Kumaun University, SSJ Campus, Almora, Uttarakhand, India
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11
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Snizhko AD, Kyrychenko AV, Gladkov ES. Synthesis of Novel Derivatives of 5,6,7,8-Tetrahydroquinazolines Using α-Aminoamidines and In Silico Screening of Their Biological Activity. Int J Mol Sci 2022; 23:ijms23073781. [PMID: 35409144 PMCID: PMC8999073 DOI: 10.3390/ijms23073781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 02/05/2023] Open
Abstract
α-Aminoamidines are promising reagents for the synthesis of a diverse family of pyrimidine ring derivatives. Here, we demonstrate the use of α-aminoamidines for the synthesis of a new series of 5,6,7,8-tetrahydroquinazolines by their reaction with bis-benzylidene cyclohexanones. The reaction occurs in mild conditions and is characterized by excellent yields. It has easy workup, as compared to the existing methods of tetrahydroquinazoline preparation. Newly synthesized derivatives of 5,6,7,8-tetrahydroquinazoline bear protecting groups at the C2-tert-butyl moiety of a quinazoline ring, which can be easily cleaved, opening up further opportunities for their functionalization. Moreover, molecular docking studies indicate that the synthesized compounds reveal high binding affinity toward some essential enzymes of Mycobacterial tuberculosis, such as dihydrofolate reductase (DHFR), pantothenate kinase (MtPanK), and FAD-containing oxidoreductase DprE1 (MtDprE1), so that they may be promising candidates for the molecular design and the development of new antitubercular agents against multidrug-resistant strains of the Tubercle bacillus. Finally, the high inhibition activity of the synthesized compounds was also predicted against β-glucosidase, suggesting a novel tetrahydroquinazoline scaffold for the treatment of diabetes.
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Affiliation(s)
- Arsenii D. Snizhko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Sq., 61022 Kharkiv, Ukraine; (A.D.S.); (A.V.K.)
| | - Alexander V. Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Sq., 61022 Kharkiv, Ukraine; (A.D.S.); (A.V.K.)
| | - Eugene S. Gladkov
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Sq., 61022 Kharkiv, Ukraine; (A.D.S.); (A.V.K.)
- State Scientific Institution “Institute for Single Crystals”, National Academy of Sciences of Ukraine, 60 Nauky Ave, 61072 Kharkiv, Ukraine
- Correspondence:
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QSAR and Molecular Docking Studies of Pyrimidine–Coumarin–Triazole Conjugates as Prospective Anti-Breast Cancer Agents. Molecules 2022; 27:molecules27061845. [PMID: 35335208 PMCID: PMC8955476 DOI: 10.3390/molecules27061845] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 02/04/2023] Open
Abstract
Cancer is a life-threatening disease and is the second leading cause of death worldwide. Although many drugs are available for the treatment of cancer, survival outcomes are very low. Hence, rapid development of newer anticancer agents is a prime focus of the medicinal chemistry community. Since the recent past, computational methods have been extensively employed for accelerating the drug discovery process. In view of this, in the present study we performed 2D-QSAR (Quantitative Structure-Activity Relationship) analysis of a series of compounds reported with potential anticancer activity against breast cancer cell line MCF7 using QSARINS software. The best four models exhibited a r2 value of 0.99. From the generated QSAR equations, a series of pyrimidine-coumarin-triazole conjugates were designed and their MCF7 cell inhibitory activities were predicted using the QSAR equations. Furthermore, molecular docking studies were carried out for the designed compounds using AutoDock Vina against dihydrofolate reductase (DHFR), colchicine and vinblastine binding sites of tubulin, the key enzyme targets in breast cancer. The most active compounds identified through these computational studies will be useful for synthesizing and testing them as prospective novel anti-breast cancer agents.
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13
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The discovery of 1, 3-diamino-7H-pyrrol[3, 2-f]quinazoline compounds as potent antimicrobial antifolates. Eur J Med Chem 2022; 228:113979. [PMID: 34802838 DOI: 10.1016/j.ejmech.2021.113979] [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: 10/05/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 12/14/2022]
Abstract
The shortage of new antibiotics makes infections caused by gram-negative (G-) bacteria a significant clinical problem. The key enzymes involved in folate biosynthesis represent important targets for drug discovery, and new antifolates with novel mechanisms are urgently needed. By targeting to dihydrofolate reductase (DHFR), a series of 1,3-diamino-7H-pyrrol[3,2-f]quinazoline (PQZ) compounds were designed, and exhibited potent antibacterial activities in vitro, especially against multi-drug resistant G- strains. Multiple experiments indicated that PQZ compounds contain a different molecular mechanism against the typical DHFR inhibitor, trimethoprim (TMP), and the thymidylate synthase (TS) was identified as another potential but a relatively weak target. A significant synergism between the representative compound, OYYF-175, and sulfamethoxazole (SMZ) was observed with a strong cumulative and significantly bactericidal effect at extremely low concentrations (2 μg/mL for SMZ and 0.03 pg/mL for OYYF-175), which could be resulted from the simultaneous inhibition of dihydropteroate synthase (DHPS), DHFR and TS. PQZ compounds exhibited therapeutic effects in a mouse model of intraperitoneal infections caused by Escherichia coli (E. coli). The co-crystal structure of OYYF-175-DHFR was solved and the detailed interactions were provided. The inhibitors reported represent innovative chemical structures with novel molecular mechanism of action, which will benefit the generation of new, efficacious bactericidal compounds.
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14
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Bundhoo E, Ghoorah AW, Jaufeerally-Fakim Y. TAGOPSIN: collating taxa-specific gene and protein functional and structural information. BMC Bioinformatics 2021; 22:517. [PMID: 34688246 PMCID: PMC8541804 DOI: 10.1186/s12859-021-04429-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 10/06/2021] [Indexed: 11/25/2022] Open
Abstract
Background The wealth of biological information available nowadays in public databases has triggered an unprecedented rise in multi-database search and data retrieval for obtaining detailed information about key functional and structural entities. This concerns investigations ranging from gene or genome analysis to protein structural analysis. However, the retrieval of interconnected data from a number of different databases is very often done repeatedly in an unsystematic way. Results Here, we present TAxonomy, Gene, Ontology, Protein, Structure INtegrated (TAGOPSIN), a command line program written in Java for rapid and systematic retrieval of select data from seven of the most popular public biological databases relevant to comparative genomics and protein structure studies. The program allows a user to retrieve organism-centred data and assemble them in a single data warehouse which constitutes a useful resource for several biological applications. TAGOPSIN was tested with a number of organisms encompassing eukaryotes, prokaryotes and viruses. For example, it successfully integrated data for about 17,000 UniProt entries of Homo sapiens and 21 UniProt entries of human coronavirus. Conclusion TAGOPSIN demonstrates efficient data integration whereby manipulation of interconnected data is more convenient than doing multi-database queries. The program facilitates for instance interspecific comparative analyses of protein-coding genes in a molecular evolutionary study, or identification of taxa-specific protein domains and three-dimensional structures. TAGOPSIN is available as a JAR file at https://github.com/ebundhoo/TAGOPSIN and is released under the GNU General Public License. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04429-5.
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Affiliation(s)
- Eshan Bundhoo
- Department of Agricultural and Food Science, Faculty of Agriculture, University of Mauritius, Reduit, 80837, Mauritius
| | - Anisah W Ghoorah
- Department of Digital Technologies, Faculty of Information, Communication and Digital Technologies, University of Mauritius, Reduit, 80837, Mauritius.
| | - Yasmina Jaufeerally-Fakim
- Department of Agricultural and Food Science, Faculty of Agriculture, University of Mauritius, Reduit, 80837, Mauritius
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15
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Ibrahim SA, Fayed EA, Rizk HF, Desouky SE, Ragab A. Hydrazonoyl bromide precursors as DHFR inhibitors for the synthesis of bis-thiazolyl pyrazole derivatives; antimicrobial activities, antibiofilm, and drug combination studies against MRSA. Bioorg Chem 2021; 116:105339. [PMID: 34530234 DOI: 10.1016/j.bioorg.2021.105339] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 08/30/2021] [Accepted: 09/05/2021] [Indexed: 01/15/2023]
Abstract
Microbial resistance is a big concern worldwide, making the development of new antimicrobial drugs difficult. The thiazole and pyrazole rings are important heterocyclic compounds utilized to produce a variety of antimicrobial medications. As a result, a series of new bis-thiazolyl-pyrazole derivatives 3, 4a-c, 5a, b, and 6a-c was synthesized by reacting bis hydrazonoyl bromide with several active methylene reagents in a one-pot reaction. The assigned structure was characterized entirely based on elemental and spectral analyses. The antimicrobial activity represented by MIC was performed using a resazurin-based turbidimetric (TB) assay. The results exhibited good antimicrobial activity against gram-positive strains, especially S. aureus (ATCC6538) while showing poor to moderate activity against gram-negative and fungal strains. Furthermore, the most active derivatives 3, 4a, 4c, and 5b were evaluated for MIC, MBC, antibiofilm, hemolytic assay, and drug combination testing against two S. aureus (ATCC6538) and MRSA (ACL18) strains. Additionally, bis-thiazolyl pyrazole 3, 4c, and 5b exhibited more potent inhibitory activity for DHFR with IC50 values (6.34 ± 0.26, 7.49 ± 0.28, and 3.81 ± 0.16 µM), respectively, compared with Trimethoprim (8.34 ± 0.11 µM). The bis-1-(substituted-thiazol-2-yl)-1H-pyrazole-4-carbonitrile derivative 5b was the most active member with MIC values ranging from (0.12-0.25 µM) compared to Vancomycin (1-2 µM), and MBC values ranging from (0.5-1 µM) for S. aureus (ATCC6538) and MRSA (ACL18). Surprisingly, compound 5b displayed bactericidal behavior, synergistic effect with three commercial antibiotics, and inhibited DHFR with 2.1 folds higher than Trimethoprim. Finally, good findings were obtained from in silico investigations incorporating toxicity prediction and molecular docking simulation.
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Affiliation(s)
- Seham A Ibrahim
- Chemistry Department, Faculty of Science, Tanta University, Tanta 31527, Egypt.
| | - Eman A Fayed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11754, Egypt
| | - Hala F Rizk
- Chemistry Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Said E Desouky
- Department of Botany and Microbiology, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Ahmed Ragab
- Chemistry Department, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo 11884, Egypt.
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16
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Wróbel A, Baradyn M, Ratkiewicz A, Drozdowska D. Synthesis, Biological Activity, and Molecular Dynamics Study of Novel Series of a Trimethoprim Analogs as Multi-Targeted Compounds: Dihydrofolate Reductase (DHFR) Inhibitors and DNA-Binding Agents. Int J Mol Sci 2021; 22:3685. [PMID: 33916202 PMCID: PMC8037161 DOI: 10.3390/ijms22073685] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/27/2021] [Accepted: 03/29/2021] [Indexed: 01/07/2023] Open
Abstract
Eighteen previously undescribed trimethoprim (TMP) analogs containing amide bonds (1-18) were synthesized and compared with TMP, methotrexate (MTX), and netropsin (NT). These compounds were designed as potential minor groove binding agents (MGBAs) and inhibitors of human dihydrofolate reductase (hDHFR). The all-new derivatives were obtained via solid phase synthesis using 4-nitrophenyl Wang resin. Data from the ethidium displacement test confirmed their DNA-binding capacity. Compounds 13-14 (49.89% and 43.85%) and 17-18 (41.68% and 42.99%) showed a higher binding affinity to pBR322 plasmid than NT. The possibility of binding in a minor groove as well as determination of association constants were performed using calf thymus DNA, T4 coliphage DNA, poly (dA-dT)2, and poly (dG-dC)2. With the exception of compounds 9 (IC50 = 56.05 µM) and 11 (IC50 = 55.32 µM), all of the compounds showed better inhibitory properties against hDHFR than standard, which confirms that the addition of the amide bond into the TMP structures increases affinity towards hDHFR. Derivatives 2, 6, 13, 14, and 16 were found to be the most potent hDHFR inhibitors. This molecular modelling study shows that they interact strongly with a catalytically important residue Glu-30.
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Affiliation(s)
- Agnieszka Wróbel
- Department of Organic Chemistry, Medical University of Bialystok, 15-222 Bialystok, Poland;
| | - Maciej Baradyn
- Department of Physical Chemistry, Institute of Chemistry, University of Bialystok, 15-245 Bialystok, Poland; (M.B.); (A.R.)
| | - Artur Ratkiewicz
- Department of Physical Chemistry, Institute of Chemistry, University of Bialystok, 15-245 Bialystok, Poland; (M.B.); (A.R.)
| | - Danuta Drozdowska
- Department of Organic Chemistry, Medical University of Bialystok, 15-222 Bialystok, Poland;
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17
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A combined structure-based pharmacophore modeling and 3D-QSAR study on a series of N-heterocyclic scaffolds to screen novel antagonists as human DHFR inhibitors. Struct Chem 2021. [DOI: 10.1007/s11224-020-01705-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Juárez-Saldivar A, Schroeder M, Salentin S, Haupt VJ, Saavedra E, Vázquez C, Reyes-Espinosa F, Herrera-Mayorga V, Villalobos-Rocha JC, García-Pérez CA, Campillo NE, Rivera G. Computational Drug Repositioning for Chagas Disease Using Protein-Ligand Interaction Profiling. Int J Mol Sci 2020; 21:ijms21124270. [PMID: 32560043 PMCID: PMC7348847 DOI: 10.3390/ijms21124270] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 02/06/2023] Open
Abstract
Chagas disease, caused by Trypanosoma cruzi (T. cruzi), affects nearly eight million people worldwide. There are currently only limited treatment options, which cause several side effects and have drug resistance. Thus, there is a great need for a novel, improved Chagas treatment. Bifunctional enzyme dihydrofolate reductase-thymidylate synthase (DHFR-TS) has emerged as a promising pharmacological target. Moreover, some human dihydrofolate reductase (HsDHFR) inhibitors such as trimetrexate also inhibit T. cruzi DHFR-TS (TcDHFR-TS). These compounds serve as a starting point and a reference in a screening campaign to search for new TcDHFR-TS inhibitors. In this paper, a novel virtual screening approach was developed that combines classical docking with protein-ligand interaction profiling to identify drug repositioning opportunities against T. cruzi infection. In this approach, some food and drug administration (FDA)-approved drugs that were predicted to bind with high affinity to TcDHFR-TS and whose predicted molecular interactions are conserved among known inhibitors were selected. Overall, ten putative TcDHFR-TS inhibitors were identified. These exhibited a similar interaction profile and a higher computed binding affinity, compared to trimetrexate. Nilotinib, glipizide, glyburide and gliquidone were tested on T. cruzi epimastigotes and showed growth inhibitory activity in the micromolar range. Therefore, these compounds could lead to the development of new treatment options for Chagas disease.
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Affiliation(s)
- Alfredo Juárez-Saldivar
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (A.J.-S.); (F.R.-E.); (V.H.-M.); (J.C.V.-R.)
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany; (M.S.); (S.S.); (V.J.H.)
| | - Sebastian Salentin
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany; (M.S.); (S.S.); (V.J.H.)
| | - V. Joachim Haupt
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany; (M.S.); (S.S.); (V.J.H.)
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de Mexico 14080, Mexico; (E.S.); (C.V.)
| | - Citlali Vázquez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de Mexico 14080, Mexico; (E.S.); (C.V.)
| | - Francisco Reyes-Espinosa
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (A.J.-S.); (F.R.-E.); (V.H.-M.); (J.C.V.-R.)
| | - Verónica Herrera-Mayorga
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (A.J.-S.); (F.R.-E.); (V.H.-M.); (J.C.V.-R.)
- Departamento de Ingeniería Bioquímica, Unidad Académica Multidisciplinaria Mante, Universidad Autónoma de Tamaulipas, Mante 89840, Mexico
| | - Juan Carlos Villalobos-Rocha
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (A.J.-S.); (F.R.-E.); (V.H.-M.); (J.C.V.-R.)
| | - Carlos A. García-Pérez
- Scientific Computing Research Unit, Helmholtz Zentrum München, 85764 Neuherberg, Germany;
| | - Nuria E. Campillo
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain;
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (A.J.-S.); (F.R.-E.); (V.H.-M.); (J.C.V.-R.)
- Correspondence: ; Tel.: +52-1-8991-601-356
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19
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He J, Qiao W, An Q, Yang T, Luo Y. Dihydrofolate reductase inhibitors for use as antimicrobial agents. Eur J Med Chem 2020; 195:112268. [PMID: 32298876 DOI: 10.1016/j.ejmech.2020.112268] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/22/2020] [Accepted: 03/22/2020] [Indexed: 02/05/2023]
Abstract
Drug-resistant bacteria pose an increasingly serious threat to mankind all over the world. However, the currently available clinical treatments do not meet the urgent demand.Therefore, it is desirable to find new targets and inhibitors to overcome the problems of antibiotic resistance. Dihydrofolate reductase (DHFR) is an important enzyme required to maintain bacterial growth, and hence inhibitors of DHFR have been proven as effective agents for treating bacterial infections. This review provides insights into the recent discovery of antimicrobial agents targeting DHFR. In particular, three pathogens, Escherichia coli (E. coli), Mycobacterium tuberculosis(Mtb) and Staphylococcus aureus(S. aureus), and research strategies are emphasized. DHFR inhibitors are expected to be good alternatives to fight bacterial infections.
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Affiliation(s)
- Juan He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Wenliang Qiao
- Lung Cancer Center, Laboratory of Lung Cancer, Western China Hospital of Sichuan University
| | - Qi An
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Tao Yang
- Laboratory of Human Diseases and Immunotherapies, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
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20
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Wróbel A, Maliszewski D, Baradyn M, Drozdowska D. Trimethoprim: An Old Antibacterial Drug as a Template to Search for New Targets. Synthesis, Biological Activity and Molecular Modeling Study of Novel Trimethoprim Analogs. Molecules 2019; 25:molecules25010116. [PMID: 31892256 PMCID: PMC6983048 DOI: 10.3390/molecules25010116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/21/2019] [Accepted: 12/24/2019] [Indexed: 01/15/2023] Open
Abstract
A new series of trimethoprim (TMP) analogs containing amide bonds (1–6) have been synthesized. Molecular docking, as well as dihydrofolate reductase (DHFR) inhibition assay were used to confirm their affinity to bind dihydrofolate reductase enzyme. Data from the ethidium displacement test showed their DNA-binding capacity. Tests confirming the possibility of DNA binding in a minor groove as well as determination of the association constants were performed using calf thymus DNA, T4 coliphage DNA, poly (dA-dT)2 and poly (dG-dC)2. Additionally, the mechanism of action of the new compounds was studied. In conclusion, some of our new analogs inhibited DHFR activity more strongly than TMP did, which confirms, that the addition of amide bonds into the analogs of TMP increases their affinity towards DHFR.
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Affiliation(s)
- Agnieszka Wróbel
- Department of Organic Chemistry, Medical University of Bialystok, 15222 Bialystok, Poland; (D.M.); (D.D.)
- Correspondence: ; Tel.: +50-253-3188
| | - Dawid Maliszewski
- Department of Organic Chemistry, Medical University of Bialystok, 15222 Bialystok, Poland; (D.M.); (D.D.)
| | - Maciej Baradyn
- Department of Physical Chemistry, University of Bialystok, Institute of Chemistry, 15245 Bialystok, Poland;
| | - Danuta Drozdowska
- Department of Organic Chemistry, Medical University of Bialystok, 15222 Bialystok, Poland; (D.M.); (D.D.)
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21
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Sharma K, Neshat N, Sharma S, Giri N, Srivastava A, Almalki F, Saifullah K, Alam MM, Shaquiquzzaman M, Akhter M. Identification of novel selective Mtb-DHFR inhibitors as antitubercular agents through structure-based computational techniques. Arch Pharm (Weinheim) 2019; 353:e1900287. [PMID: 31867798 DOI: 10.1002/ardp.201900287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/01/2019] [Accepted: 12/08/2019] [Indexed: 12/23/2022]
Abstract
Inhibition of dihydrofolate reductase from Mycobacterium tuberculosis-dihydrofolate reductase (Mtb-DHFR) has emerged as a promising approach for the treatment of tuberculosis. To identify novel Mtb-DHFR inhibitors, structure-based virtual screening (SBVS) of the Molecular Diversity Preservation International (MolMall) database was performed using Glide against the Mtb-DHFR and h-DHFR enzymes. On the basis of SBVS, receptor fit, drug-like filters, and ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis, 16 hits were selected and tested for their antitubercular activity against the H37 RV strain of M. tuberculosis. Five compounds showed promising activity with compounds 11436 and 15275 as the most potent hits with IC50 values of 0.65 and 12.51 μM, respectively, against the H37 RV strain of M. tuberculosis. The two compounds were further tested in the Mtb-DHFR and h-DHFR enzymatic assay for selectivity and were found to be three- to eight-fold selective towards Mtb-DHFR over h-DHFR with minimum inhibitory concentration values of 5.50, 73.89 µM and 42.00, 263.00 µM, respectively. In silico simulation studies also supported the stability of the protein-ligand complex formation. The present study demonstrates the successful utilization of in silico SBVS tools for the identification of novel and potential Mtb-DHFR inhibitors and compound 11436 ((2,4-dihydroxyphenyl)(3,4,5-trihydroxyphenyl)methanone) as a potential lead for the development of novel Mtb-DHFR inhibitors.
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Affiliation(s)
- Kalicharan Sharma
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | - Nazia Neshat
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | - Shweta Sharma
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | - Namita Giri
- Department of Pharmaceutical Sciences, Ferris State University, Big Rapids, Michigan
| | - Apeksha Srivastava
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | - Faisal Almalki
- College of Pharmacy, Umm Al-Qura University, Mecca, Kingdom of Saudi Arabia
| | - Khalid Saifullah
- College of Pharmacy, Umm Al-Qura University, Mecca, Kingdom of Saudi Arabia
| | - Md Mumtaz Alam
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India
| | | | - Mymoona Akhter
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi, India.,Bioinformatics Infrastructure Facility, Jamia Hamdard, New Delhi, India
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22
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Pharmacoinformatics-based identification of anti-bacterial catalase-peroxidase enzyme inhibitors. Comput Biol Chem 2019; 83:107136. [DOI: 10.1016/j.compbiolchem.2019.107136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/28/2019] [Accepted: 09/29/2019] [Indexed: 11/17/2022]
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Trimethoprim and other nonclassical antifolates an excellent template for searching modifications of dihydrofolate reductase enzyme inhibitors. J Antibiot (Tokyo) 2019; 73:5-27. [PMID: 31578455 PMCID: PMC7102388 DOI: 10.1038/s41429-019-0240-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/07/2019] [Accepted: 08/22/2019] [Indexed: 12/17/2022]
Abstract
The development of new mechanisms of resistance among pathogens, the occurrence and transmission of genes responsible for antibiotic insensitivity, as well as cancer diseases have been a serious clinical problem around the world for over 50 years. Therefore, intense searching of new leading structures and active substances, which may be used as new drugs, especially against strain resistant to all available therapeutics, is very important. Dihydrofolate reductase (DHFR) has attracted a lot of attention as a molecular target for bacterial resistance over several decades, resulting in a number of useful agents. Trimethoprim (TMP), (2,4-diamino-5-(3′,4′,5′-trimethoxybenzyl)pyrimidine) is the well-known dihydrofolate reductase inhibitor and one of the standard antibiotics used in urinary tract infections (UTIs). This review highlights advances in design, synthesis, and biological evaluations in structural modifications of TMP as DHFR inhibitors. In addition, this report presents the differences in the active site of human and pathogen DHFR. Moreover, an excellent review of DHFR inhibition and their relevance to antimicrobial and parasitic chemotherapy was presented.
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Ribeiro JA, Chavez-Pacheco SM, de Oliveira GS, Silva CDS, Giudice JHP, Libreros-Zúñiga GA, Dias MVB. Crystal structures of the closed form of Mycobacterium tuberculosis dihydrofolate reductase in complex with dihydrofolate and antifolates. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:682-693. [PMID: 31282477 DOI: 10.1107/s205979831900901x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 06/24/2019] [Indexed: 12/19/2022]
Abstract
Tuberculosis is a disease caused by Mycobacterium tuberculosis and is the leading cause of death from a single infectious pathogen, with a high prevalence in developing countries in Africa and Asia. There still is a need for the development or repurposing of novel therapies to combat this disease owing to the long-term nature of current therapies and because of the number of reported resistant strains. Here, structures of dihydrofolate reductase from M. tuberculosis (MtDHFR), which is a key target of the folate pathway, are reported in complex with four antifolates, pyrimethamine, cycloguanil, diaverdine and pemetrexed, and its substrate dihydrofolate in order to understand their binding modes. The structures of all of these complexes were obtained in the closed-conformation state of the enzyme and a fine structural analysis indicated motion in key regions of the substrate-binding site and different binding modes of the ligands. In addition, the affinities, through Kd measurement, of diaverdine and methotrexate have been determined; MtDHFR has a lower affinity (highest Kd) for diaverdine than pyrimethamine and trimethoprim, and a very high affinity for methotrexate, as expected. The structural comparisons and analysis described in this work provide new information about the plasticity of MtDHFR and the binding effects of different antifolates.
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Affiliation(s)
- João Augusto Ribeiro
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Sair Maximo Chavez-Pacheco
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Gabriel Stephani de Oliveira
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Catharina Dos Santos Silva
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - João Henrique Pimenta Giudice
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Gerardo Andres Libreros-Zúñiga
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Marcio Vinicius Bertacine Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
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Cantini F, Niccoli L, Capone A, Petrone L, Goletti D. Risk of tuberculosis reactivation associated with traditional disease modifying anti-rheumatic drugs and non-anti-tumor necrosis factor biologics in patients with rheumatic disorders and suggestion for clinical practice. Expert Opin Drug Saf 2019; 18:415-425. [PMID: 31066297 DOI: 10.1080/14740338.2019.1612872] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Two classes of biologics, anti-tumor necrosis factor (TNF) and non-anti-TNF targeted, are currently available for the treatment of rheumatic diseases. AREAS COVERED Discussion on the need for LTBI diagnosis in rheumatic patients treated csDMARDs and non-anti-TNFs through a review of the literature. The literature, updated to 15 April 2019, on tuberculosis (TB) reactivation risk in patients exposed to conventional synthetic disease-modifying antirheumatic drugs (csDMARDs) and non-anti-TNF biologics was reviewed. EXPERT OPINION An increased risk of TB reactivation in patients receiving csDMARDs (except sulphasalazine) resulted, while a review of clinical trials, and Periodic Safety Update Reports from pharmaceutical Companies evidenced a very low or absent risk for non-anti-TNF biologics. Hence, a contradiction emerges considering that latent TB infection (LTBI) screening is recommended for non-anti-TNF candidates but not for csDMARDs. Concerning the low TB incidence countries, several actions could be undertaken, including to screen all patients independently on the treatment, to omit the procedure in non-anti-TNF candidates, or to perform the LTBI investigations only in high-risk patients. According to WHO guidelines, LTBI screening in low TB risk countries seems unnecessary, except in high TB risk subjects.
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Affiliation(s)
- Fabrizio Cantini
- a Department of Rheumatology , Hospital of Prato , Prato , Italy
| | - Laura Niccoli
- a Department of Rheumatology , Hospital of Prato , Prato , Italy
| | - Alessandro Capone
- b Clinical Department , National Institute for Infectious Diseases L. Spallanzani-IRCCS , Rome , Italy
| | - Linda Petrone
- c Translational Research Unit, Department of Epidemiology and Preclinical Research , "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS , Rome , Italy
| | - Delia Goletti
- c Translational Research Unit, Department of Epidemiology and Preclinical Research , "L. Spallanzani" National Institute for Infectious Diseases (INMI), IRCCS , Rome , Italy
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Sharma K, Tanwar O, Deora GS, Ali S, Alam MM, Zaman MS, Krishna VS, Sriram D, Akhter M. Expansion of a novel lead targeting M. tuberculosis DHFR as antitubercular agents. Bioorg Med Chem 2019; 27:1421-1429. [PMID: 30827867 DOI: 10.1016/j.bmc.2019.02.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 01/26/2023]
Abstract
A series of 1-(1-benzyl-2-methyl-5-((1-phenyl-1H-1,2,3-triazol-4-yl)methoxy)-1H-indol-3-yl)ethanone and ethyl 1-benzyl-2-methyl-5-((1-phenyl-1H-1,2,3-triazol-4-yl)methoxy)-1H-indole-3-carboxylate derivatives were designed based on bioisosteric replacement of previously reported antitubercular agent (IND-07). Twenty ligands were successfully synthesized and some of them were found to have good in vitro activity (MIC < 10 μM) against the H37Rv strain of Mycobacterium tuberculosis. Among these compounds, KC-08 and KC-11 inhibited Mtb-DHFR with 4- and 18-fold selectivity for Mtb-DHFR over h-DHFR, respectively. Compound KC-11 display acceptable ADME, and better pharmacokinetic profiles than IND-07. Docking studies were performed to predict the binding mode of the compounds within the active site of Mtb-DHFR and h-DHFR. The results of our study suggest that compound KC-11 may serve as a valuable lead for the design and development of selective inhibitors of Mtb-DHFR with potential therapeutic application in tuberculosis.
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Affiliation(s)
- Kalicharan Sharma
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India
| | - Omprakash Tanwar
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India
| | - Girdhar Singh Deora
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - S Ali
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi 110062, India; Bioinformatics Infrastructure Facility Lab, Jamia Hamdard, New Delhi 110062, India
| | - M M Alam
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India
| | - M S Zaman
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India
| | - Vagolu Siva Krishna
- Department of Pharmacy, Birla Institute of Technology & Science, Pilani, Hyderabad 500078, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology & Science, Pilani, Hyderabad 500078, India
| | - Mymoona Akhter
- Department of Pharmaceutical Chemistry, SPER, Jamia Hamdard, New Delhi 110062, India; Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi 110062, India.
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27
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Sharma K, Tanwar O, Sharma S, Ali S, Alam M, Zaman M, Akhter M. Structural comparison of Mtb-DHFR and h-DHFR for design, synthesis and evaluation of selective non-pteridine analogues as antitubercular agents. Bioorg Chem 2018; 80:319-333. [DOI: 10.1016/j.bioorg.2018.04.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/18/2018] [Accepted: 04/24/2018] [Indexed: 11/29/2022]
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Synthesis of 2,4-Diaminopyrimidine Core-Based Derivatives and Biological Evaluation of Their Anti-Tubercular Activities. Molecules 2017; 22:molecules22101592. [PMID: 28937657 PMCID: PMC6151568 DOI: 10.3390/molecules22101592] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis (TB) is a chronic, potentially fatal disease caused by Mycobacterium tuberculosis (Mtb). The dihyrofolate reductase in Mtb (mt-DHFR) is believed to be an important drug target in anti-TB drug development. This enzyme contains a glycerol (GOL) binding site, which is assumed to be a useful site to improve the selectivity towards human dihyrofolate reductase (h-DHFR). There have been previous attempts to design drugs targeting the GOL binding site, but the designed compounds contain a hydrophilic group, which may prevent the compounds from crossing the cell wall of Mtb to function at the whole cell level. In the current study, we designed and synthesized a series of mt-DHFR inhibitors that contain a 2,4-diaminopyrimidine core with side chains to occupy the glycerol binding site with proper hydrophilicity for cell entry, and tested their anti-tubercular activity against Mtb H37Ra. Among them, compound 16l showed a good anti-TB activity (MIC = 6.25 μg/mL) with a significant selectivity against vero cells. In the molecular simulations performed to understand the binding poses of the compounds, it was noticed that only side chains of a certain size can occupy the glycerol binding site. In summary, the novel synthesized compounds with appropriate side chains, hydrophobicity and selectivity could be important lead compounds for future optimization towards the development of future anti-TB drugs that can be used as monotherapy or in combination with other anti-TB drugs or antibiotics. These compounds can also provide much information for further studies on mt-DHFR. However, the enzyme target of the compounds still needs to be confirmed by pure mt-DHFR binding assays.
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Santa Maria JP, Park Y, Yang L, Murgolo N, Altman MD, Zuck P, Adam G, Chamberlin C, Saradjian P, Dandliker P, Boshoff HIM, Barry CE, Garlisi C, Olsen DB, Young K, Glick M, Nickbarg E, Kutchukian PS. Linking High-Throughput Screens to Identify MoAs and Novel Inhibitors of Mycobacterium tuberculosis Dihydrofolate Reductase. ACS Chem Biol 2017; 12:2448-2456. [PMID: 28806050 DOI: 10.1021/acschembio.7b00468] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Though phenotypic and target-based high-throughput screening approaches have been employed to discover new antibiotics, the identification of promising therapeutic candidates remains challenging. Each approach provides different information, and understanding their results can provide hypotheses for a mechanism of action (MoA) and reveal actionable chemical matter. Here, we describe a framework for identifying efficacy targets of bioactive compounds. High throughput biophysical profiling against a broad range of targets coupled with machine learning was employed to identify chemical features with predicted efficacy targets for a given phenotypic screen. We validate the approach on data from a set of 55 000 compounds in 24 historical internal antibacterial phenotypic screens and 636 bacterial targets screened in high-throughput biophysical binding assays. Models were built to reveal the relationships between phenotype, target, and chemotype, which recapitulated mechanisms for known antibacterials. We also prospectively identified novel inhibitors of dihydrofolate reductase with nanomolar antibacterial efficacy against Mycobacterium tuberculosis. Molecular modeling provided structural insight into target-ligand interactions underlying selective killing activity toward mycobacteria over human cells.
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Affiliation(s)
- John P. Santa Maria
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Yumi Park
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Lihu Yang
- Department of Chemistry, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Nicholas Murgolo
- Department of Information & Analytics, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Michael D. Altman
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Paul Zuck
- Research Science, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Greg Adam
- Department of Pharmacology, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Chad Chamberlin
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Saradjian
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Dandliker
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Helena I. M. Boshoff
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Clifton E. Barry
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Charles Garlisi
- Department of Pharmacology, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - David B. Olsen
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Katherine Young
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Meir Glick
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Elliott Nickbarg
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter S. Kutchukian
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
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30
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Hajian B, Scocchera E, Keshipeddy S, G-Dayanandan N, Shoen C, Krucinska J, Reeve S, Cynamon M, Anderson AC, Wright DL. Propargyl-Linked Antifolates Are Potent Inhibitors of Drug-Sensitive and Drug-Resistant Mycobacterium tuberculosis. PLoS One 2016; 11:e0161740. [PMID: 27580226 PMCID: PMC5006990 DOI: 10.1371/journal.pone.0161740] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/10/2016] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis continues to cause widespread, life-threatening disease. In the last decade, this threat has grown dramatically as multi- and extensively-drug resistant (MDR and XDR) bacteria have spread globally and the number of agents that effectively treat these infections is significantly reduced. We have been developing the propargyl-linked antifolates (PLAs) as potent inhibitors of the essential enzyme dihydrofolate reductase (DHFR) from bacteria and recently found that charged PLAs with partial zwitterionic character showed improved mycobacterial cell permeability. Building on a hypothesis that these PLAs may penetrate the outer membrane of M. tuberculosis and inhibit the essential cytoplasmic DHFR, we screened a group of PLAs for antitubercular activity. In this work, we identified several PLAs as potent inhibitors of the growth of M. tuberculosis with several of the compounds exhibiting minimum inhibition concentrations equal to or less than 1 μg/mL. Furthermore, two of the compounds were very potent inhibitors of MDR and XDR strains. A high resolution crystal structure of one PLA bound to DHFR from M. tuberculosis reveals the interactions of the ligands with the target enzyme.
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Affiliation(s)
- Behnoush Hajian
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Eric Scocchera
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Santosh Keshipeddy
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Narendran G-Dayanandan
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Carolyn Shoen
- Veterans Affairs Medical Center, Syracuse, New York, United States of America
| | - Jolanta Krucinska
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Stephanie Reeve
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Michael Cynamon
- Veterans Affairs Medical Center, Syracuse, New York, United States of America
| | - Amy C. Anderson
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail: (ACA); (DLW)
| | - Dennis L. Wright
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail: (ACA); (DLW)
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31
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(±)-Japonones A and B, two pairs of new enantiomers with anti-KSHV activities from Hypericum japonicum. Sci Rep 2016; 6:27588. [PMID: 27270221 PMCID: PMC4897785 DOI: 10.1038/srep27588] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/20/2016] [Indexed: 11/08/2022] Open
Abstract
Two pairs of new enantiomers with unusual 5,5-spiroketal cores, termed (±)-japonones A and B [(±)-1 and (±)-2], were obtained from Hypericum japonicum Thunb. The absolute configurations of (±)-1 and (±)-2 were characterized by extensive analyses of spectroscopic data and calculated electronic circular dichroism (ECD) spectra, the application of modified Mosher’s methods, and the assistance of quantum chemical predictions (QCP) of 13C NMR chemical shifts. Among these metabolites, (+)-1 exhibited some inhibitory activity on Kaposi’s sarcoma associated herpesvirus (KSHV). Virtual screening of (±)-1 and (±)-2 were conducted using the Surflex-Dock module in the Sybyl software, and (+)-1 exhibited ability to bind with ERK to form key interactions with residues Lys52, Pro56, Ile101, Asp165, Gly167 and Val99.
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32
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dfrA thyA Double Deletion in para-Aminosalicylic Acid-Resistant Mycobacterium tuberculosis Beijing Strains. Antimicrob Agents Chemother 2016; 60:3864-7. [PMID: 27021327 PMCID: PMC4879365 DOI: 10.1128/aac.00253-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Nyíri K, Vértessy BG. Perturbation of genome integrity to fight pathogenic microorganisms. Biochim Biophys Acta Gen Subj 2016; 1861:3593-3612. [PMID: 27217086 DOI: 10.1016/j.bbagen.2016.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Resistance against antibiotics is unfortunately still a major biomedical challenge for a wide range of pathogens responsible for potentially fatal diseases. SCOPE OF REVIEW In this study, we aim at providing a critical assessment of the recent advances in design and use of drugs targeting genome integrity by perturbation of thymidylate biosynthesis. MAJOR CONCLUSION We find that research efforts from several independent laboratories resulted in chemically highly distinct classes of inhibitors of key enzymes within the routes of thymidylate biosynthesis. The present article covers numerous studies describing perturbation of this metabolic pathway in some of the most challenging pathogens like Mycobacterium tuberculosis, Plasmodium falciparum, and Staphylococcus aureus. GENERAL SIGNIFICANCE Our comparative analysis allows a thorough summary of the current approaches to target thymidylate biosynthesis enzymes and also include an outlook suggesting novel ways of inhibitory strategies. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Kinga Nyíri
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
| | - Beáta G Vértessy
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
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34
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Gandhi PT, Athmaram TN, Arunkumar GR. Novel nicotine analogues with potential anti-mycobacterial activity. Bioorg Med Chem 2016; 24:1637-47. [PMID: 26951892 DOI: 10.1016/j.bmc.2016.02.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/18/2016] [Accepted: 02/25/2016] [Indexed: 02/01/2023]
Abstract
Tuberculosis (TB) is the second leading lethal infectious disease in the world after acquired immuno deficiency (AIDs). We have developed a series of twenty-five novel nicotine analogues with de-addiction property and tested them for their activity against Mycobacterium tuberculosis (MTB). In an effort to increase the specificity of action and directing nicotine analogues to target MTB, four promising compounds were further optimized via molecular docking studies against the Dihydrofolate reductase of MTB. After lead optimization, one nicotine analogue [3-(5-(3fluorophenyl)nicotinoyl)-1-methylpyrrolidin-2-one] exhibited minimum inhibitory concentration of 1 μg/mL (2.86 nM) against M. tuberculosis (H37Rv strain), a human pathogenic strain of clinically significant importance. Pharmacokinetic analysis of [3-(5-(3fluorophenyl)nicotinoyl)-1methylpyrrolidin-2-one] with lowest MIC value via oral route in Wistar rats revealed that at a dosage of 5 mg/kg body weight gave a maximum serum drug concentration (Cmax) of 2.86 μg/mL, Tmax of one hour and a half-life (T1/2) of more than 24 h and Volume of distribution (Vd) of 27.36 L. Whereas the parenteral (intra venous) route showed a Cmax of 3.37 μg/mL, Tmax of 0.05 h, T1/2 of 24 h and Vd equivalent to 23.18 L. The acute oral toxicity and repeated oral toxicity studies in female Wistar rats had an LD50>2000 mg/kg body weight. Our data suggests that nicotine derivatives developed in the present study has good metabolic stability with tunable pharmacokinetics (PK) with therapeutic potential to combat MTB. However, further in vivo studies for anti-tuberculosis activity and elucidation of mode of action could result in more promising novel drug for treating MTB. To the best of our knowledge this is the first report revealing the anti-mycobacterial potential of nicotine analogue at potential therapeutic concentrations.
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Affiliation(s)
- Paresh T Gandhi
- Advance Research Products, LLC, 608, 21st Avenue, Paterson, NJ 07513, USA
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