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Chan BWGL, Lynch NB, Tran W, Joyce JM, Savage GP, Meutermans W, Montgomery AP, Kassiou M. Fragment-based drug discovery for disorders of the central nervous system: designing better drugs piece by piece. Front Chem 2024; 12:1379518. [PMID: 38698940 PMCID: PMC11063241 DOI: 10.3389/fchem.2024.1379518] [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: 01/31/2024] [Accepted: 03/12/2024] [Indexed: 05/05/2024] Open
Abstract
Fragment-based drug discovery (FBDD) has emerged as a powerful strategy to confront the challenges faced by conventional drug development approaches, particularly in the context of central nervous system (CNS) disorders. FBDD involves the screening of libraries that comprise thousands of small molecular fragments, each no greater than 300 Da in size. Unlike the generally larger molecules from high-throughput screening that limit customisation, fragments offer a more strategic starting point. These fragments are inherently compact, providing a strong foundation with good binding affinity for the development of drug candidates. The minimal elaboration required to transition the hit into a drug-like molecule is not only accelerated, but also it allows for precise modifications to enhance both their activity and pharmacokinetic properties. This shift towards a fragment-centric approach has seen commercial success and holds considerable promise in the continued streamlining of the drug discovery and development process. In this review, we highlight how FBDD can be integrated into the CNS drug discovery process to enhance the exploration of a target. Furthermore, we provide recent examples where FBDD has been an integral component in CNS drug discovery programs, enabling the improvement of pharmacokinetic properties that have previously proven challenging. The FBDD optimisation process provides a systematic approach to explore this vast chemical space, facilitating the discovery and design of compounds piece by piece that are capable of modulating crucial CNS targets.
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Affiliation(s)
| | - Nicholas B. Lynch
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Wendy Tran
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | - Jack M. Joyce
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
| | | | | | | | - Michael Kassiou
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
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2
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Saah SA, Sakyi PO, Adu-Poku D, Boadi NO, Djan G, Amponsah D, Devine RNOA, Ayittey K. Docking and Molecular Dynamics Identify Leads against 5 Alpha Reductase 2 for Benign Prostate Hyperplasia Treatment. J CHEM-NY 2023. [DOI: 10.1155/2023/8880213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Steroid 5 alpha-reductase 2 (5αR-2) is a membrane-embedded protein that together with other isoforms plays a key role in the metabolism of steroids. This enzyme catalyzes the reduction of testosterone to the more potent ligand, dihydrotestosterone (DHT) in the prostate. Androgens, testosterone, and DHT play important roles in prostate growth, development, and function. At the same time, both testosterone and DHT have been implicated in the pathogenesis of benign prostate hyperplasia (BPH). Inhibition of the DHT formation, therefore, provides a therapeutic strategy that offers the possibility of preventing, delaying, or treating BPH. Currently, two steroidal drugs that inhibit 5αR-2, dutasteride and finasteride, have been approved for clinical use. These two come at a high cost and also portray undesirable sexual side effects which necessitate the need to find new chemotherapeutic alternatives for the disease. Based on the aforementioned, finasteride and dutasteride were subjected to scaffold hopping, fragment-based de novo design, molecular docking, and molecular dynamics simulations employing databases like ChEMBL, DrugBank, PubChem, ChemSpider, and Zinc15 in the identification of potential hits targeting 5αR-2. Altogether, ten novel compounds targeting 5αR-2 were identified with binding energies lower or comparable to finasteride and dutasteride, the main inhibitors for this target. Molecular docking and molecular dynamics simulations studies identify amino acid residues Glu57, Phe219, Phe223, and Leu224 to be critical for ligand binding and complex stability. The physicochemical and pharmacological profiling suggests the potential of the hit compounds to be drug-like and orally active. Similarly, the quality parameter assessments revealed the hits possess LELP greater than 3 implying their promise as lead-like molecules. The compounds A5, A9, and A10 were, respectively, predicted to treat prostate disorders with Pa (0.188, 0.361, and 0.270) and Pi (0.176, 0.050, and 0.093), while A8 and A9 were found to be associated with BPH treatment with Pa (0.09 and 0.127) and Pi (0.077 and 0.033), respectively. Structural similarity searches via DrugBank identified the drugs faropenem, acemetacin, estradiol valerate, and yohimbine to be useful for BPH treatment suggesting the de novo designed ligands as potential chemotherapeutic agents for treating this disease.
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3
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Beteck RM, Isaacs M, Legoabe LJ, Hoppe HC, Tam CC, Kim JH, Petzer JP, Cheng LW, Quiambao Q, Land KM, Khanye SD. Synthesis and in vitro antiprotozoal evaluation of novel metronidazole-Schiff base hybrids. Arch Pharm (Weinheim) 2023; 356:e2200409. [PMID: 36446720 DOI: 10.1002/ardp.202200409] [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: 08/03/2022] [Revised: 10/10/2022] [Accepted: 11/03/2022] [Indexed: 12/05/2022]
Abstract
Herein we report the synthesis of 21 novel small molecules inspired by metronidazole and Schiff base compounds. The compounds were evaluated against Trichomonas vaginalis and cross-screened against other pathogenic protozoans of clinical relevance. Most of these compounds were potent against T. vaginalis, exhibiting IC50 values < 5 µM. Compound 20, the most active compound against T. vaginalis, exhibited an IC50 value of 3.4 µM. A few compounds also exhibited activity against Plasmodium falciparum and Trypanosomal brucei brucei, with compound 6 exhibiting an IC50 value of 0.7 µM against P. falciparum and compound 22 exhibiting an IC50 value of 1.4 µM against T.b. brucei. Compound 22 is a broad-spectrum antiprotozoal agent, showing activities against all three pathogenic protozoans under investigation.
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Affiliation(s)
- Richard M Beteck
- Department of Pharmaceutical Chemistry, Centre of Excellence for Pharmaceutical Sciences (Pharmacen), North-West University, Potchefstroom, South Africa
| | - Michelle Isaacs
- Centre for Chemico- and Biomedical Research, Rhodes University, Makhanda, South Africa
| | - Lesetja J Legoabe
- Department of Pharmaceutical Chemistry, Centre of Excellence for Pharmaceutical Sciences (Pharmacen), North-West University, Potchefstroom, South Africa
| | - Heinrich C Hoppe
- Centre for Chemico- and Biomedical Research, Rhodes University, Makhanda, South Africa.,Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Christina C Tam
- Foodborne Toxin Detection and Prevention Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, California, USA
| | - Jong H Kim
- Foodborne Toxin Detection and Prevention Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, California, USA
| | - Jacobus P Petzer
- Department of Pharmaceutical Chemistry, Centre of Excellence for Pharmaceutical Sciences (Pharmacen), North-West University, Potchefstroom, South Africa
| | - Luisa W Cheng
- Foodborne Toxin Detection and Prevention Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, California, USA
| | - Quincel Quiambao
- Department of Biological Sciences, University of the Pacific, Stockton, California, USA
| | - Kirkwood M Land
- Department of Biological Sciences, University of the Pacific, Stockton, California, USA
| | - Setshaba D Khanye
- Centre for Chemico- and Biomedical Research, Rhodes University, Makhanda, South Africa.,Division of Pharmaceutical Chemistry, Faculty of Pharmacy, Rhodes University, Makhanda, South Africa
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4
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Carmichael N, Day PJR. Cell Surface Transporters and Novel Drug Developments. Front Pharmacol 2022; 13:852938. [PMID: 35350751 PMCID: PMC8957865 DOI: 10.3389/fphar.2022.852938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
Despite the numerous scientific and technological advances made within the last decade the attrition rates for new drug discovery remain as high as 95% for anticancer drugs. Recent drug development has been in part guided by Lipinski’s Rule of 5 (Ro5) even though many approved drugs do not comply to these rules. With Covid-19 vaccine development strategy dramatically accelerating drug development perhaps it is timely to question the generic drug development process itself to find a more efficient, cost effective, and successful approach. It is widely believed that drugs permeate cells via two methods: phospholipid bilayer diffusion and carrier mediated transporters. However, emerging evidence suggests that carrier mediated transport may be the primary mechanism of drug uptake and not diffusion as long believed. Computational biology increasingly assists drug design to achieve desirable absorption, distribution, metabolism, elimination and toxicity (ADMET) properties. Perfecting drug entry into target cells as a prerequisite to intracellular drug action is a logical and compelling route and is expected to reduce drug attrition rates, particularly gaining favour amongst chronic lifelong therapeutics. Novel drug development is rapidly expanding from the utilisation of beyond the rule of five (bRo5) to pulsatile drug delivery systems and fragment based drug design. Utilising transporters as drug targets and advocating bRo5 molecules may be the solution to increasing drug specificity, reducing dosage and toxicity and thus revolutionising drug development. This review explores the development of cell surface transporter exploitation in drug development and the relationship with improved therapeutic index.
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Affiliation(s)
- Natasha Carmichael
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Philip J R Day
- School of Biological Sciences and Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Thabet FM, Dawood KM, Ragab EA, Nafie MS, Abbas AA. Design and synthesis of new bis(1,2,4-triazolo[3,4- b][1,3,4]thiadiazines) and bis((quinoxalin-2-yl)phenoxy)alkanes as anti-breast cancer agents through dual PARP-1 and EGFR targets inhibition. RSC Adv 2022; 12:23644-23660. [PMID: 36090415 PMCID: PMC9389373 DOI: 10.1039/d2ra03549a] [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: 06/08/2022] [Accepted: 08/10/2022] [Indexed: 12/01/2022] Open
Abstract
A number of new 1,ω-bis((acetylphenoxy)acetamide)alkanes 5a–f were prepared then their bromination using NBS furnished the novel bis(2-bromoacetyl)phenoxy)acetamides 6a–f. Reaction of 6a–f with 4-amino-5-substituted-4H-1,2,4-triazole-3-thiol 7a–d and with o-phenylenediamine derivatives 9a and b afforded the corresponding bis(1,2,4-triazolo[3,4-b][1,3,4]thiadiazine) derivatives 8a–l and bis(quinoxaline) derivatives 10a–e in good yields. The cytotoxicity of the synthesized compounds as well as apoptosis induction through PARP-1 and EGFR as molecular targets was evaluated. Three compounds, 8d, 8i and 8l, exhibited much better cytotoxic activities against MDA-MB-231 than the drug Erlotinib. Interestingly, compound 8i induced apoptosis in MDA-MB-231 cells by 38-fold compared to the control arresting the cell cycle at the G2/M phase, and its treatment upregulated P53, Bax, caspase-3, caspase-8, and caspase-9 gene levels, while it downregulated the Bcl2 level. Compound 8i exhibited promising dual enzyme inhibition of PARP-1 (IC50 = 1.37 nM) compared to Olaparib (IC50 = 1.49 nM), and EGFR (IC50 = 64.65 nM) compared to Erlotinib (IC50 = 80 nM). These results agreed with the molecular docking studies that highlighted the binding disposition of compound 8i inside the PARP-1 and EGFR protein active sites. Hence, compound 8i may serve as a potential anti-breast cancer agent. A series of bis(triazolothiadiazines) and bis(quinoxalines) were synthesized and tested for their cytotoxicity and apoptosis-induction through PARP-1 and EGFR as molecular targets. Compound 8i exhibited high cytotoxic activity and promising dual enzyme inhibition.![]()
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Affiliation(s)
- Fatma M. Thabet
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Kamal M. Dawood
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Eman A. Ragab
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Mohamed S. Nafie
- Department of Chemistry, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| | - Ashraf A. Abbas
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
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6
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Dangi M, Khichi A, Jakhar R, Chhillar AK. Growing Preferences towards Analog-based Drug Discovery. Curr Pharm Biotechnol 2021; 22:1030-1045. [PMID: 32900347 DOI: 10.2174/1389201021666200908121409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/29/2020] [Accepted: 08/21/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The major concern of today's time is the developing resistance in most of the clinically derived pathogenic micro-organisms for available drugs through several mechanisms. Therefore, there is a dire need to develop novel molecules with drug-like properties that can be effective against the otherwise resistant micro-organisms. METHODS New drugs can be developed using several methods like structure-based drug design, ligandbased drug design, or by developing analogs of the available drugs to further improve their effects. However, the smartness is to opt for the techniques that have comparatively less expenditure, lower failure rates, and faster discovery rates. RESULTS Analog-Based Drug Design (ABDD) is one such technique that researchers worldwide are opting to develop new drug-like molecules with comparatively lower market values. They start by first designing the analogs sharing structural and pharmacological similarities to the existing drugs. This method embarks on scaffold structures of available drugs already approved by the clinical trials, but are left ineffective because of resistance developed by the pathogens. CONCLUSION In this review, we have discussed some recent examples of anti-fungal and anti-bacterial (antimicrobial) drugs that were designed based on the ABDD technique. Also, we have tried to focus on the in silico tools and techniques that can contribute to the designing and computational screening of the analogs, so that these can be further considered for in vitro screening to validate their better biological activities against the pathogens with comparatively reduced rates of failure.
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Affiliation(s)
- Mehak Dangi
- Centre for Bioinformatics, M.D. University, Rohtak-124001, Haryana, India
| | - Alka Khichi
- Centre for Bioinformatics, M.D. University, Rohtak-124001, Haryana, India
| | - Ritu Jakhar
- Centre for Bioinformatics, M.D. University, Rohtak-124001, Haryana, India
| | - Anil K Chhillar
- Centre for Bioinformatics, M.D. University, Rohtak-124001, Haryana, India
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6-amide-2-aryl benzoxazole/benzimidazole derivatives as VEFGR-2 inhibitors in two-and three-dimensional QSAR studies: topomer CoMFA and HQSAR. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01588-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Diethelm-Varela B. Using NMR Spectroscopy in the Fragment-Based Drug Discovery of Small-Molecule Anticancer Targeted Therapies. ChemMedChem 2020; 16:725-742. [PMID: 33236493 DOI: 10.1002/cmdc.202000756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/21/2020] [Indexed: 12/19/2022]
Abstract
Against the challenge of providing personalized cancer care, the development of targeted therapies stands as a promising approach. The discovery of these agents can benefit from fragment-based drug discovery (FBDD) methods that help guide ligand design and provide key structural information on the targets of interest. In particular, nuclear magnetic resonance spectroscopy is a promising biophysical tool in fragment discovery due to its detection capabilities and versatility. This review provides an overview of FBDD, describes the basis of NMR-based fragment screening, summarizes some exciting technical advances reported over the past decades, and closes with a discussion of selected case studies where this technique has been used as part of drug discovery campaigns to produce lead compounds towards the design of anti-cancer targeted therapies.
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Affiliation(s)
- Benjamin Diethelm-Varela
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD 21201, USA
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9
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Rosenbaum MI, Clemmensen LS, Bredt DS, Bettler B, Strømgaard K. Targeting receptor complexes: a new dimension in drug discovery. Nat Rev Drug Discov 2020; 19:884-901. [PMID: 33177699 DOI: 10.1038/s41573-020-0086-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2020] [Indexed: 12/11/2022]
Abstract
Targeting receptor proteins, such as ligand-gated ion channels and G protein-coupled receptors, has directly enabled the discovery of most drugs developed to modulate receptor signalling. However, as the search for novel and improved drugs continues, an innovative approach - targeting receptor complexes - is emerging. Receptor complexes are composed of core receptor proteins and receptor-associated proteins, which have profound effects on the overall receptor structure, function and localization. Hence, targeting key protein-protein interactions within receptor complexes provides an opportunity to develop more selective drugs with fewer side effects. In this Review, we discuss our current understanding of ligand-gated ion channel and G protein-coupled receptor complexes and discuss strategies for their pharmacological modulation. Although such strategies are still in preclinical development for most receptor complexes, they exemplify how receptor complexes can be drugged, and lay the groundwork for this nascent area of research.
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Affiliation(s)
- Mette Ishøy Rosenbaum
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Louise S Clemmensen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - David S Bredt
- Neuroscience Discovery, Janssen Pharmaceutical Companies of Johnson & Johnson, San Diego, CA, USA
| | - Bernhard Bettler
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
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10
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Shanmugam A, Muralidharan N, Velmurugan D, Gromiha MM. Therapeutic Targets and Computational Approaches on Drug Development for COVID-19. Curr Top Med Chem 2020; 20:2210-2220. [DOI: 10.2174/1568026620666200710105507] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/20/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022]
Abstract
World Health Organization declared coronavirus disease (COVID-19) caused by SARS
coronavirus-2 (SARS-CoV-2) as pandemic. Its outbreak started in China in Dec 2019 and rapidly spread
all over the world. SARS-CoV-2 has infected more than 800,000 people and caused about 35,000 deaths
so far, moreover, no approved drugs are available to treat COVID-19. Several investigations have been
carried out to identify potent drugs for COVID-19 based on drug repurposing, potential novel compounds
from ligand libraries, natural products, short peptides, and RNAseq analysis. This review is focused
on three different aspects; (i) targets for drug design (ii) computational methods to identify lead
compounds and (iii) drugs for COVID-19. It also covers the latest literature on various hit molecules
proposed by computational methods and experimental techniques.
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Affiliation(s)
- Anusuya Shanmugam
- Department of Pharmaceutical Engineering, Vinayaka Mission’s KirupanandaVariyar Engineering College, Vinayaka Mission’s Research Foundation (Deemed to be University), Salem – 636308, Tamil Nadu, India
| | - Nisha Muralidharan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai – 600036, Tamil Nadu, India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai - 600025, India
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai – 600036, Tamil Nadu, India
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Gutti G, Kumar D, Paliwal P, Ganeshpurkar A, Lahre K, Kumar A, Krishnamurthy S, Singh SK. Development of pyrazole and spiropyrazoline analogs as multifunctional agents for treatment of Alzheimer's disease. Bioorg Chem 2019; 90:103080. [PMID: 31271946 DOI: 10.1016/j.bioorg.2019.103080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/11/2019] [Accepted: 06/18/2019] [Indexed: 12/31/2022]
Abstract
Cholinergic hypothesis of Alzheimer's disease has been advocated as an essential tool in the last couple of decades for the drug development. Here in, we report de novo fragment growing strategy for the design of novel 3,5-diarylpyrazoles and hit optimization of spiropyrazoline derivatives as acetyl cholinesterase inhibitors. Both type of scaffolds numbering forty compounds were synthesized and evaluated for their potencies against AChE, BuChE and PAMPA. Introduction of lipophilic cyclohexane ring in 3,5-diarylpyrazole analogs led to spiropyrazoline derivatives, which facilitated and improved the potencies. Compound 44 (AChE = 1.937 ± 0.066 µM; BuChE = 1.166 ± 0.088 µM; hAChE = 1.758 ± 0.095 µM; Pe = 9.491 ± 0.34 × 10-6 cm s1) showed positive results, which on further optimization led to the development of compound 67 (AChE = 0.464 ± 0.166 µM; BuChE = 0.754 ± 0.121 µM; hAChE = 0.472 ± 0.042 µM; Pe = 13.92 ± 0.022 × 10-6 cm s1). Compounds 44 and 67 produced significant displacement of propidium iodide from the peripheral anionic site (PAS) of AChE. They were found to be safer to MC65 cells and decreased metal induced Aβ1-42 aggregation. Further, in-vivo behavioral studies, on scopolamine induced amnesia model, the compounds resulted in better percentage spontaneous alternation scores and were safe, had no influence on locomotion in tested animal groups at dose of 3 mg/kg. Early pharmacokinetic assessment of optimized hit molecules was supportive for further drug development.
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Affiliation(s)
- Gopichand Gutti
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Devendra Kumar
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Pankaj Paliwal
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Ankit Ganeshpurkar
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Khemraj Lahre
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Ashok Kumar
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Sairam Krishnamurthy
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Sushil Kumar Singh
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India.
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12
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Kuhn S, Johnson SR. Stereo-Aware Extension of HOSE Codes. ACS OMEGA 2019; 4:7323-7329. [PMID: 31459832 PMCID: PMC6648302 DOI: 10.1021/acsomega.9b00488] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/02/2019] [Indexed: 05/16/2023]
Abstract
Descriptions of molecular environments have many applications in chemoinformatics, including chemical shift prediction. Hierarchically ordered spherical environment (HOSE) codes are the most popular such descriptions. We developed a method to extend these with stereochemistry information. It enables distinguishing atoms which would be considered identical in traditional HOSE codes. The use of our method is demonstrated by chemical shift predictions for molecules in the nmrshiftdb2 database. We give a full specification and an implementation.
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Affiliation(s)
- Stefan Kuhn
- School
of Computer Science and Informatics, De
Montfort University, The Gateway LE1 9BH, Leicester, U.K.
- E-mail:
| | - Sean R. Johnson
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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13
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Yu J, Zhu X, Harvey PJ, Kaas Q, Zhangsun D, Craik DJ, Luo S. Single Amino Acid Substitution in α-Conotoxin TxID Reveals a Specific α3β4 Nicotinic Acetylcholine Receptor Antagonist. J Med Chem 2018; 61:9256-9265. [DOI: 10.1021/acs.jmedchem.8b00967] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jinpeng Yu
- Key Laboratory of Tropical Biological Resources, Ministry of Education; Key Laboratory for Marine Drugs of Haikou, Hainan University, Haikou 570228, China
| | - Xiaopeng Zhu
- Key Laboratory of Tropical Biological Resources, Ministry of Education; Key Laboratory for Marine Drugs of Haikou, Hainan University, Haikou 570228, China
| | - Peta J. Harvey
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Dongting Zhangsun
- Key Laboratory of Tropical Biological Resources, Ministry of Education; Key Laboratory for Marine Drugs of Haikou, Hainan University, Haikou 570228, China
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sulan Luo
- Key Laboratory of Tropical Biological Resources, Ministry of Education; Key Laboratory for Marine Drugs of Haikou, Hainan University, Haikou 570228, China
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14
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Identification of Antifungal Targets Based on Computer Modeling. J Fungi (Basel) 2018; 4:jof4030081. [PMID: 29973534 PMCID: PMC6162656 DOI: 10.3390/jof4030081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/24/2018] [Accepted: 06/29/2018] [Indexed: 01/07/2023] Open
Abstract
Aspergillus fumigatus is a saprophytic, cosmopolitan fungus that attacks patients with a weak immune system. A rational solution against fungal infection aims to manipulate fungal metabolism or to block enzymes essential for Aspergillus survival. Here we discuss and compare different bioinformatics approaches to analyze possible targeting strategies on fungal-unique pathways. For instance, phylogenetic analysis reveals fungal targets, while domain analysis allows us to spot minor differences in protein composition between the host and fungi. Moreover, protein networks between host and fungi can be systematically compared by looking at orthologs and exploiting information from host⁻pathogen interaction databases. Further data—such as knowledge of a three-dimensional structure, gene expression data, or information from calculated metabolic fluxes—refine the search and rapidly put a focus on the best targets for antimycotics. We analyzed several of the best targets for application to structure-based drug design. Finally, we discuss general advantages and limitations in identification of unique fungal pathways and protein targets when applying bioinformatics tools.
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15
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NMR-Fragment Based Virtual Screening: A Brief Overview. Molecules 2018; 23:molecules23020233. [PMID: 29370102 PMCID: PMC6017141 DOI: 10.3390/molecules23020233] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/12/2017] [Accepted: 12/12/2017] [Indexed: 01/23/2023] Open
Abstract
Fragment-based drug discovery (FBDD) using NMR has become a central approach over the last twenty years for development of small molecule inhibitors against biological macromolecules, to control a variety of cellular processes. Yet, several considerations should be taken into account for obtaining a therapeutically relevant agent. In this review, we aim to list the considerations that make NMR fragment screening a successful process for yielding potent inhibitors. Factors that may govern the competence of NMR in fragment based drug discovery are discussed, as well as later steps that involve optimization of hits obtained by NMR-FBDD.
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Chino A, Seo R, Amano Y, Namatame I, Hamaguchi W, Honbou K, Mihara T, Yamazaki M, Tomishima M, Masuda N. Fragment-Based Discovery of Pyrimido[1,2- b]indazole PDE10A Inhibitors. Chem Pharm Bull (Tokyo) 2018; 66:286-294. [DOI: 10.1248/cpb.c17-00836] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Ayaka Chino
- Drug Discovery Research, Astellas Pharma Inc
| | - Ryushi Seo
- Drug Discovery Research, Astellas Pharma Inc
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Wang ZF, Wang PF, Ma JT, Chai YZ, Hu HM, Gao WL, Wang ZC, Wang BZ, Zhu HL. Design of potent B-RafV600Einhibitors by multiple copy simulation search strategy. Chem Biol Drug Des 2017; 91:567-574. [DOI: 10.1111/cbdd.13121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/24/2017] [Accepted: 09/23/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Ze-Feng Wang
- State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing China
| | - Peng-Fei Wang
- State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing China
| | - Jun-Ting Ma
- State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing China
| | - Ying-Zi Chai
- State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing China
| | - Hui-Min Hu
- State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing China
| | - Wen-Long Gao
- State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing China
| | - Zhong-Chang Wang
- State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing China
| | - Bao-Zhong Wang
- State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology; Nanjing University; Nanjing China
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Jamkhande PG, Ghante MH, Ajgunde BR. Software based approaches for drug designing and development: A systematic review on commonly used software and its applications. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.bfopcu.2017.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Wang J, Li W, Wang B, Hu B, Jiang H, Lai B, Li N, Cheng M. In Silicon Approach for Discovery of Chemopreventive Agents. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40495-017-0094-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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20
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Cottingham C, Che P, Zhang W, Wang H, Wang RX, Percival S, Birky T, Zhou L, Jiao K, Wang Q. Diverse arrestin-recruiting and endocytic profiles of tricyclic antipsychotics acting as direct α 2A adrenergic receptor ligands. Neuropharmacology 2016; 116:38-49. [PMID: 27956055 DOI: 10.1016/j.neuropharm.2016.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 11/28/2016] [Accepted: 12/08/2016] [Indexed: 01/01/2023]
Abstract
The therapeutic mechanism of action underlying many psychopharmacological agents remains poorly understood, due largely to the extreme molecular promiscuity exhibited by these agents with respect to potential central nervous system targets. Agents of the tricyclic chemical class, including both antidepressants and antipsychotics, exhibit a particularly high degree of molecular promiscuity; therefore, any clarification of how these agents interact with specific central nervous system targets is of great potential significance to the field. Here, we present evidence demonstrating that tricyclic antipsychotics appear to segregate into three distinct groups based upon their molecular interactions with the centrally-important α2A adrenergic receptor (AR). Specifically, while the α2AAR binds all antipsychotics tested with similar affinities, and none of the agents are able to induce classical heterotrimeric G protein-mediated α2AAR signaling, significant differences are observed with respect to arrestin3 recruitment and receptor endocytosis. All antipsychotics tested induce arrestin3 recruitment to the α2AAR, but with differing strengths. Both chlorpromazine and clozapine drive significant α2AAR endocytosis, but via differing clathrin-dependent and lipid raft-dependent pathways, while fluphenazine does not drive a robust response. Intriguingly, in silico molecular modeling suggests that each of the three exhibits unique characteristics in interacting with the α2AAR ligand-binding pocket. In addition to establishing these three antipsychotics as novel arrestin-biased ligands at the α2AAR, our findings provide key insights into the molecular actions of these clinically-important agents.
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Affiliation(s)
- Christopher Cottingham
- Department of Cell, Molecular and Developmental Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Department of Biology and Chemistry, Morehead State University, Morehead, KY 40351, USA
| | - Pulin Che
- Department of Cell, Molecular and Developmental Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Wei Zhang
- Southern Research Institute, Birmingham, AL 35205, USA
| | - Hongxia Wang
- Department of Cell, Molecular and Developmental Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Raymond X Wang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stefanie Percival
- Department of Cell, Molecular and Developmental Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Tana Birky
- Department of Cell, Molecular and Developmental Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lufang Zhou
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kai Jiao
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Qin Wang
- Department of Cell, Molecular and Developmental Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Identification of DNA primase inhibitors via a combined fragment-based and virtual screening. Sci Rep 2016; 6:36322. [PMID: 27805033 PMCID: PMC5090872 DOI: 10.1038/srep36322] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/14/2016] [Indexed: 11/12/2022] Open
Abstract
The structural differences between bacterial and human primases render the former an excellent target for drug design. Here we describe a technique for selecting small molecule inhibitors of the activity of T7 DNA primase, an ideal model for bacterial primases due to their common structural and functional features. Using NMR screening, fragment molecules that bind T7 primase were identified and then exploited in virtual filtration to select larger molecules from the ZINC database. The molecules were docked to the primase active site using the available primase crystal structure and ranked based on their predicted binding energies to identify the best candidates for functional and structural investigations. Biochemical assays revealed that some of the molecules inhibit T7 primase-dependent DNA replication. The binding mechanism was delineated via NMR spectroscopy. Our approach, which combines fragment based and virtual screening, is rapid and cost effective and can be applied to other targets.
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Immunomodulatory Effects Mediated by Dopamine. J Immunol Res 2016; 2016:3160486. [PMID: 27795960 PMCID: PMC5067323 DOI: 10.1155/2016/3160486] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 07/29/2016] [Accepted: 08/08/2016] [Indexed: 01/11/2023] Open
Abstract
Dopamine (DA), a neurotransmitter in the central nervous system (CNS), has modulatory functions at the systemic level. The peripheral and central nervous systems have independent dopaminergic system (DAS) that share mechanisms and molecular machinery. In the past century, experimental evidence has accumulated on the proteins knowledge that is involved in the synthesis, reuptake, and transportation of DA in leukocytes and the differential expression of the D1-like (D1R and D5R) and D2-like receptors (D2R, D3R, and D4R). The expression of these components depends on the state of cellular activation and the concentration and time of exposure to DA. Receptors that are expressed in leukocytes are linked to signaling pathways that are mediated by changes in cAMP concentration, which in turn triggers changes in phenotype and cellular function. According to the leukocyte lineage, the effects of DA are associated with such processes as respiratory burst, cytokine and antibody secretion, chemotaxis, apoptosis, and cytotoxicity. In clinical conditions such as schizophrenia, Parkinson disease, Tourette syndrome, and multiple sclerosis (MS), there are evident alterations during immune responses in leukocytes, in which changes in DA receptor density have been observed. Several groups have proposed that these findings are useful in establishing clinical status and clinical markers.
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