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Hussein BRM, Moustafa AH, Abdou A, Drar AM, Abdel-Raheem SAA. Preparation, Agricultural Bioactivity Evaluation, Structure-Activity Relationships Estimation, and Molecular Docking of Some Quinazoline Compounds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38597922 DOI: 10.1021/acs.jafc.3c08840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Quinazoline compounds have gained significant attention in the fields of agriculture and chemistry due to their diverse activities. In this study, we focused on a series of quinazoline derivatives (4a-l). The objectives involved multiple aspects, including preparation, evaluation of their agricultural bioactivity against the maize aphid (Rhopalosiphum maidis), estimation of the structure-activity relationships (SAR), and conducting molecular docking analysis. The results of the agricultural bioactivities revealed that compound (4b) possesses the highest insecticidal activity, and the other compounds have good potential as insecticidal agents. We conducted the SARs and also molecular docking investigation to elucidate the binding modes and interactions of these compounds with target proteins relevant to the agricultural bioactivity. The docking results provided valuable information on the binding affinities and molecular interactions, aiding in the rationalization of the observed bioactivity trends. The enzyme, acetylcholinesterase (AChE), was docked with the 12 synthetic compounds (4a-l). Among these compounds, (4b), (4i), and (4e)exhibited the highest binding affinity, with docking scores (S) of -7.96, -7.83, and -7.73 kcal/mol, respectively. They were followed by compounds (4d) (S = -7.57 kcal/mol), (4c) (S = -7.53 kcal/mol), (4g) (S = -7.34 kcal/mol), (4f) (S = -7.23 kcal/mol), (4h) (S = -7.14 kcal/mol), (4k) (S = -6.61 kcal/mol), (4j) (S = -6.57 kcal/mol), (4a) (S = -6.28 kcal/mol), and finally (4l) (S = -6.01 kcal/mol). These compounds were shown to have a variety of binding interactions within the 2ACE active site, as evidenced by protein-ligand docking configurations. This study gives evidence that those compounds have AChE-inhibitory capabilities and, hence, may be used for AChE-targeting development. Also, the findings in this study highlight the potential of these compounds as agricultural agents and provide valuable insights for the design and development of some quinazoline derivatives with enhanced bioactivity for crop protection.
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Affiliation(s)
- Bahgat R M Hussein
- Department of Chemistry, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | - Amr H Moustafa
- Department of Chemistry, Faculty of Science, Sohag University, Sohag 82524, Egypt
- Faculty of Science, King Salman International University, Rassudr, Sinai 46612, Egypt
| | - Aly Abdou
- Department of Chemistry, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | - Ali M Drar
- Plant Protection Research Institute, Agricultural Research Center, Dokki, Giza 12619, Egypt
| | - Shaban A A Abdel-Raheem
- Soils, Water, and Environment Research Institute, Agricultural Research Center, Giza 12112, Egypt
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Zaib S, Areeba, Khan I. Purinergic Signaling and its Role in the Stem Cell Differentiation. Mini Rev Med Chem 2024; 24:863-883. [PMID: 37828668 DOI: 10.2174/0113895575261206231003151416] [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: 05/07/2023] [Revised: 07/30/2023] [Accepted: 08/30/2023] [Indexed: 10/14/2023]
Abstract
Purinergic signaling is a mechanism in which extracellular purines and pyrimidines interact with specialized cell surface receptors known as purinergic receptors. These receptors are divided into two families of P1 and P2 receptors, each responding to different nucleosides and nucleotides. P1 receptors are activated by adenosine, while P2 receptors are activated by pyrimidine and purines. P2X receptors are ligand-gated ion channels, including seven subunits (P2X1-7). However, P2Y receptors are the G-protein coupled receptors comprising eight subtypes (P2Y1/2/4/6/11/12/13/14). The disorder in purinergic signaling leads to various health-related issues and diseases. In various aspects, it influences the activity of non-neuronal cells and neurons. The molecular mechanism of purinergic signaling provides insight into treating various human diseases. On the contrary, stem cells have been investigated for therapeutic applications. Purinergic signaling has shown promising effect in stem cell engraftment. The immune system promotes the autocrine and paracrine mechanisms and releases the significant factors essential for successful stem cell therapy. Each subtype of purinergic receptor exerts a beneficial effect on the damaged tissue. The most common effect caused by purinergic signaling is the proliferation and differentiation that treat different health-related conditions.
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Affiliation(s)
- Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590, Pakistan
| | - Areeba
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590, Pakistan
| | - Imtiaz Khan
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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Almikhlafi MA, Karami MM, Jana A, Alqurashi TM, Majrashi M, Alghamdi BS, Ashraf GM. Mitochondrial Medicine: A Promising Therapeutic Option Against Various Neurodegenerative Disorders. Curr Neuropharmacol 2023; 21:1165-1183. [PMID: 36043795 PMCID: PMC10286591 DOI: 10.2174/1570159x20666220830112408] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 07/14/2022] [Indexed: 11/22/2022] Open
Abstract
Abnormal mitochondrial morphology and metabolic dysfunction have been observed in many neurodegenerative disorders (NDDs). Mitochondrial dysfunction can be caused by aberrant mitochondrial DNA, mutant nuclear proteins that interact with mitochondria directly or indirectly, or for unknown reasons. Since mitochondria play a significant role in neurodegeneration, mitochondriatargeted therapies represent a prosperous direction for the development of novel drug compounds that can be used to treat NDDs. This review gives a brief description of how mitochondrial abnormalities lead to various NDDs such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. We further explore the promising therapeutic effectiveness of mitochondria- directed antioxidants, MitoQ, MitoVitE, MitoPBN, and dimebon. We have also discussed the possibility of mitochondrial gene therapy as a therapeutic option for these NDDs.
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Affiliation(s)
- Mohannad A. Almikhlafi
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Madinah, Saudi Arabia
| | - Mohammed M. Karami
- Department of Physiology, Neuroscience Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ankit Jana
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Thamer M. Alqurashi
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed Majrashi
- Department of Pharmacology, Faculty of Medicine, University of Jeddah, Jeddah, Saudi Arabia
| | - Badrah S. Alghamdi
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- The Neuroscience Research Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ghulam Md. Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, University City, Sharjah 27272, United Arab Emirates
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Neuroprotective Effects of the Psychoactive Compound Biatractylolide (BD) in Alzheimer's Disease. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238294. [PMID: 36500385 PMCID: PMC9737891 DOI: 10.3390/molecules27238294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/19/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022]
Abstract
Mitochondria play a central role in the survival or death of neuronal cells, and they are regulators of energy metabolism and cell death pathways. Many studies support the role of mitochondrial dysfunction and oxidative damage in the pathogenesis of Alzheimer's disease. Biatractylolide (BD) is a kind of internal symmetry double sesquiterpene novel ester compound isolated from the Chinese medicinal plant Baizhu, has neuroprotective effects in Alzheimer's disease. We developed a systematic pharmacological model based on chemical pharmacokinetic and pharmacological data to identify potential compounds and targets of Baizhu. The neuroprotective effects of BD in PC12 (rat adrenal pheochromocytoma cells) and SH-SY5Y (human bone marrow neuroblastoma cells) were evaluated by in vitro experiments. Based on the predicted results, we selected 18 active compounds, which were associated with 20 potential targets and 22 signaling pathways. Compound-target, target-disease and target-pathway networks were constructed using Cytoscape 3.2.1. And verified by in vitro experiments that BD could inhibit Aβ by reducing oxidative stress and decreasing CytC release induced mPTP opening. This study provides a theoretical basis for the development of BD as an anti-Alzheimer's disease drug.
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Mineyeva IV, Faletrov YV, Staravoitava VA, Shkumatov VM. Synthesis and In Silico Prediction of Biological Activity and Acute Toxicity of [1,3]Thiazolo[3,2-a]pyrimidines Containing Aliphatic Aldehyde Fragments. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1070428022070028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Puopolo T, Liu C, Ma H, Seeram NP. Inhibitory Effects of Cannabinoids on Acetylcholinesterase and Butyrylcholinesterase Enzyme Activities. Med Cannabis Cannabinoids 2022; 5:85-94. [PMID: 35702400 PMCID: PMC9149358 DOI: 10.1159/000524086] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/12/2022] [Indexed: 08/02/2023] Open
Abstract
INTRODUCTION Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) are two cholinergic enzymes catalyzing the reaction of cleaving acetylcholine into acetate and choline at the neuromuscular junction. Abnormal hyperactivity of AChE and BChE can lead to cholinergic deficiency, which is associated with several neurological disorders including cognitive decline and memory impairments. Preclinical studies support that some cannabinoids including cannabidiol (CBD) and tetrahydrocannabinol (THC) may exert pharmacological effects on the cholinergic system, but it remains unclear whether cannabinoids can inhibit AChE and BChE activities. Herein, we aimed to evaluate the inhibitory effects of a panel of cannabinoids including CBD, Δ8-THC, cannabigerol (CBG), cannabigerolic acid (CBGA), cannabicitran (CBT), cannabidivarin (CBDV), cannabichromene (CBC), and cannabinol (CBN) on AChE and BChE activities. METHODS The inhibitory effects of cannabinoids on the activities of AChE and BChE enzymes were evaluated with the Ellman method using acetyl- and butyryl-thiocholines as substrates. The inhibition mechanism of cannabinoids on AChE and BChE was studied with enzyme kinetic assays including the Lineweaver-Burk and Michaelis-Menten analyses. In addition, computational-based molecular docking experiments were performed to explore the interactions between the cannabinoids and the enzyme proteins. RESULTS Cannabinoids including CBD, Δ8-THC, CBG, CBGA, CBT, CBDV, CBC, and CBN (at 200 µM) inhibited the activities of AChE and BChE by 70.8, 83.7, 92.9, 76.7, 66.0, 79.3, 13.7, and 30.5%, and by 86.8, 80.8, 93.2, 87.1, 77.0, 78.5, 27.9, and 22.0%, respectively. The inhibitory effects of these cannabinoids (with IC50 values ranging from 85.2 to >200 µM for AChE and 107.1 to >200 µM for BChE) were less potent as compared to the positive control galantamine (IC50 1.21 and 6.86 µM for AChE and BChE, respectively). In addition, CBD, as a representative cannabinoid, displayed a competitive type of inhibition on both AChE and BChE. Data from the molecular docking studies suggested that cannabinoids interacted with several amino acid residues on the enzyme proteins, which supported their overall inhibitory effects on AChE and BChE. CONCLUSION Cannabinoids showed moderate inhibitory effects on the activities of AChE and BChE enzymes, which may contribute to their modulatory effects on the cholinergic system. Further studies using cell-based and in vivo models are warranted to evaluate whether cannabinoids' neuroprotective effects are associated with their anti-cholinesterase activities.
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Affiliation(s)
- Tess Puopolo
- Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
- George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, Rhode Island, USA
| | - Chang Liu
- Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
| | - Hang Ma
- Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
- George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, Rhode Island, USA
| | - Navindra P. Seeram
- Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
- George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, Rhode Island, USA
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De Boer D, Nguyen N, Mao J, Moore J, Sorin EJ. A Comprehensive Review of Cholinesterase Modeling and Simulation. Biomolecules 2021; 11:580. [PMID: 33920972 PMCID: PMC8071298 DOI: 10.3390/biom11040580] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/08/2021] [Accepted: 04/11/2021] [Indexed: 01/18/2023] Open
Abstract
The present article reviews published efforts to study acetylcholinesterase and butyrylcholinesterase structure and function using computer-based modeling and simulation techniques. Structures and models of both enzymes from various organisms, including rays, mice, and humans, are discussed to highlight key structural similarities in the active site gorges of the two enzymes, such as flexibility, binding site location, and function, as well as differences, such as gorge volume and binding site residue composition. Catalytic studies are also described, with an emphasis on the mechanism of acetylcholine hydrolysis by each enzyme and novel mutants that increase catalytic efficiency. The inhibitory activities of myriad compounds have been computationally assessed, primarily through Monte Carlo-based docking calculations and molecular dynamics simulations. Pharmaceutical compounds examined herein include FDA-approved therapeutics and their derivatives, as well as several other prescription drug derivatives. Cholinesterase interactions with both narcotics and organophosphate compounds are discussed, with the latter focusing primarily on molecular recognition studies of potential therapeutic value and on improving our understanding of the reactivation of cholinesterases that are bound to toxins. This review also explores the inhibitory properties of several other organic and biological moieties, as well as advancements in virtual screening methodologies with respect to these enzymes.
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Affiliation(s)
- Danna De Boer
- Department of Chemistry & Biochemistry, California State University, Long Beach, CA 90840, USA;
| | - Nguyet Nguyen
- Department of Chemical Engineering, California State University, Long Beach, CA 90840, USA; (N.N.); (J.M.)
| | - Jia Mao
- Department of Chemical Engineering, California State University, Long Beach, CA 90840, USA; (N.N.); (J.M.)
| | - Jessica Moore
- Department of Biomedical Engineering, California State University, Long Beach, CA 90840, USA;
| | - Eric J. Sorin
- Department of Chemistry & Biochemistry, California State University, Long Beach, CA 90840, USA;
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Manzoor S, Prajapati SK, Majumdar S, Raza MK, Gabr MT, Kumar S, Pal K, Rashid H, Kumar S, Krishnamurthy S, Hoda N. Discovery of new phenyl sulfonyl-pyrimidine carboxylate derivatives as the potential multi-target drugs with effective anti-Alzheimer's action: Design, synthesis, crystal structure and in-vitro biological evaluation. Eur J Med Chem 2021; 215:113224. [PMID: 33582578 DOI: 10.1016/j.ejmech.2021.113224] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 12/31/2022]
Abstract
Alzheimer's disease (AD) is multifactorial, progressive neurodegeneration with impaired behavioural and cognitive functions. The multitarget-directed ligand (MTDL) strategies are promising paradigm in drug development, potentially leading to new possible therapy options for complex AD. Herein, a series of novel MTDLs phenylsulfonyl-pyrimidine carboxylate (BS-1 to BS-24) derivatives were designed and synthesized for AD treatment. All the synthesized compounds were validated by 1HNMR, 13CNMR, HRMS, and BS-19 were structurally validated by X-Ray single diffraction analysis. To evaluate the plausible binding affinity of designed compounds, molecular docking study was performed, and the result revealed their significant interaction with active sites of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). The synthesized compounds displayed moderate to excellent in vitro enzyme inhibitory activity against AChE and BuChE at nanomolar (nM) concentration. Among 24 compounds (BS-1 to BS-24), the optimal compounds (BS-10 and BS-22) displayed potential inhibition against AChE; IC50 = 47.33 ± 0.02 nM and 51.36 ± 0.04 nM and moderate inhibition against BuChE; IC50 = 159.43 ± 0.72 nM and 153.3 ± 0.74 nM respectively. In the enzyme kinetics study, the compound BS-10 displayed non-competitive inhibition of AChE with Ki = 8 nM. Respective compounds BS-10 and BS-22 inhibited AChE-induced Aβ1-42 aggregation in thioflavin T-assay at 10 μM and 20 μM, but BS-10 at 10 μM and 20 μM concentrations are found more potent than BS-22. In addition, the aggregation properties were determined by the dynamic light scattering (DLS) and was found that BS-10 and BS-22 could significantly inhibit self-induced as well as AChE-induced Aβ1-42 aggregation. The effect of compounds (BS-10 and BS-22) on the viability of MC65 neuroblastoma cells and their capability to cross the blood-brain barrier (BBB) in PAMPA-BBB were further studied. Further, in silico approach was applied to analyze physicochemical and pharmacokinetics properties of the designed compounds via the SwissADME and PreADMET server. Hence, the novel phenylsulfonyl-pyrimidine carboxylate derivatives can act as promising leads in the development of AChE inhibitors and Aβ disaggregator for the treatment of AD.
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Affiliation(s)
- Shoaib Manzoor
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Santosh Kumar Prajapati
- Neurotherapeutics Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, U.P, 221005, India
| | - Shreyasi Majumdar
- Neurotherapeutics Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, U.P, 221005, India
| | - Md Kausar Raza
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Moustafa T Gabr
- Department of Radiology, Stanford University, Stanford, CA, 94305, United States
| | - Shivani Kumar
- University School of Biotechnology Guru Gobind Singh Indraprastha University Dwarka, Sector 16C, New Delhi, 110078, India
| | - Kavita Pal
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Haroon Rashid
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Suresh Kumar
- University School of Biotechnology Guru Gobind Singh Indraprastha University Dwarka, Sector 16C, New Delhi, 110078, India
| | - Sairam Krishnamurthy
- Neurotherapeutics Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, U.P, 221005, India.
| | - Nasimul Hoda
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India.
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Bhatia V, Sharma S. Role of mitochondrial dysfunction, oxidative stress and autophagy in progression of Alzheimer's disease. J Neurol Sci 2020; 421:117253. [PMID: 33476985 DOI: 10.1016/j.jns.2020.117253] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 10/21/2020] [Accepted: 11/24/2020] [Indexed: 12/18/2022]
Abstract
Alzheimer's disease (AD) is the most common form of dementia. The pathological hallmarks of AD are amyloid plaques [aggregates of amyloid beta (A)] and neurofibrillary tangles (aggregates of tau protein). Growing evidence suggests that tau accumulation is pathologically more relevant to the development of neurodegeneration and cognitive decline in AD patients than A plaques. Mitochondrial damage plays an important role in AD. Mitochondrial damage has been related to amyloid-beta or tau pathology or to the presence of specific presenilin-1 mutations. Elevate reactive oxygen species/reactive nitrogen species production and defective mitochondrial dynamic balance has been suggested to be the reason as well as the consequence of AD related pathology. Oxidative stress is a prominent early event in the pathogenesis of AD and is therefore believed to contribute to tau hyperphosphorylation. Several studies have shown that the autophagy pathway in neurons is important under physiological and pathological conditions. Therefore, this pathway plays a crucial role for the degradation of endogenous soluble tau. However, the relationship between mitochondrial dysfunctioning, oxidative stress, autophagy dysregulation, and neuronal cell death in AD remains unclear. Here, we review the latest progress in AD, with a special emphasis on mitochondrial dysfunctioning, oxidative stress, and autophagy. We also discuss the interlink mechanism of these three factors in AD.
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Affiliation(s)
- Vandana Bhatia
- School of Pharmaceutical and Healthcare, CT University, Ludhiana, Punjab, India
| | - Saurabh Sharma
- School of Pharmaceutical Sciences, CT University, Ludhiana, Punjab, India.
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Marondedze EF, Govender KK, Govender PP. Ligand-based pharmacophore modelling and virtual screening for the identification of amyloid-beta diagnostic molecules. J Mol Graph Model 2020; 101:107711. [DOI: 10.1016/j.jmgm.2020.107711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 07/17/2020] [Accepted: 08/04/2020] [Indexed: 01/26/2023]
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Sadeghian B, Sakhteman A, Faghih Z, Nadri H, Edraki N, Iraji A, Sadeghian I, Rezaei Z. Design, synthesis and biological activity evaluation of novel carbazole-benzylpiperidine hybrids as potential anti Alzheimer agents. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Targeting of Perforin Inhibitor into the Brain Parenchyma Via a Prodrug Approach Can Decrease Oxidative Stress and Neuroinflammation and Improve Cell Survival. Mol Neurobiol 2020; 57:4563-4577. [PMID: 32754897 PMCID: PMC7515946 DOI: 10.1007/s12035-020-02045-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/28/2020] [Indexed: 12/31/2022]
Abstract
The cytolytic protein perforin has a crucial role in infections and tumor surveillance. Recently, it has also been associated with many brain diseases, such as neurodegenerative diseases and stroke. Therefore, inhibitors of perforin have attracted interest as novel drug candidates. We have previously reported that converting a perforin inhibitor into an L-type amino acid transporter 1 (LAT1)-utilizing prodrug can improve the compound’s brain drug delivery not only across the blood–brain barrier (BBB) but also into the brain parenchymal cells: neurons, astrocytes, and microglia. The present study evaluated whether the increased uptake into mouse primary cortical astrocytes and subsequently improvements in the cellular bioavailability of this brain-targeted perforin inhibitor prodrug could enhance its pharmacological effects, such as inhibition of production of caspase-3/-7, lipid peroxidation products and prostaglandin E2 (PGE2) in the lipopolysaccharide (LPS)-induced neuroinflammation mouse model. It was demonstrated that increased brain and cellular drug delivery could improve the ability of perforin inhibitors to elicit their pharmacological effects in the brain at nano- to picomolar levels. Furthermore, the prodrug displayed multifunctional properties since it also inhibited the activity of several key enzymes related to Alzheimer’s disease (AD), such as the β-site amyloid precursor protein (APP) cleaving enzyme 1 (BACE1), acetylcholinesterase (AChE), and most probably also cyclooxygenases (COX) at micromolar concentrations. Therefore, this prodrug is a potential drug candidate for preventing Aβ-accumulation and ACh-depletion in addition to combatting neuroinflammation, oxidative stress, and neural apoptosis within the brain. Graphical abstract ![]()
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Minovski N, Saçan MT, Eminoğlu EM, Erdem SS, Novič M. Revisiting fish toxicity of active pharmaceutical ingredients: Mechanistic insights from integrated ligand-/structure-based assessments on acetylcholinesterase. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 170:548-558. [PMID: 30572250 DOI: 10.1016/j.ecoenv.2018.11.099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
The release of active pharmaceutical ingredients (APIs) into the environment is of great concern for aquatic ecosystem as many of these chemicals are designed to exert biological activity. Hence, their impact on non-target organisms like fish would not be surprising. In this respect, we revisited fish toxicity data of pharmaceuticals to generate linear and non-linear quantitative structure-toxicity relationships (QSTRs). We predicted fish lethality data from the validated QSTR models for 120 APIs with no experimental fish toxicity data. Toxicity of APIs on aquatic organisms is not fully characterized. Therefore, to provide a mechanistic insight for the assessment of API's toxicity to fish, the outcome of the derived QSTR models was integrated with structure-based toxicophore and molecular docking studies, utilizing the biomarker enzyme acetylcholinesterase originating from fish Torpedo californica (TcAChE). Toxicophore virtual screening of 60 chemicals with pT > 0 identified 23 hits as potential TcAChE binders with binding free energies ranging from -6.5 to -12.9 kcal/mol. The TcAChE-ligand interaction analysis revealed a good nesting of all 23 hits within TcAChE binding site through establishing strong lipophilic and hydrogen bonding interactions with the surrounding key amino acid residues. Among the chemicals passing the criteria of our integrated approach, majority of APIs belong noticeably to the Central Nervous System class. The screened chemicals displayed not only comprehensive toxicophore coverage, but also strong binding affinities according to the docking calculations, mainly due to interactions with TcAChE's key amino acid residues Tyr121, Tyr130, Tyr334, Trp84, Phe290, Phe330, Phe331, Ser122, and Ser200. Moreover, we propose here that binding of pharmaceuticals to AChE might have a potential in triggering molecular initiating events for adverse outcome pathways (AOPs), which in turn can play an important role for future screening of APIs lacking fish lethality data.
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Affiliation(s)
- Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
| | - Melek Türker Saçan
- Institute of Environmental Sciences, Bogazici University, 34342, Hisar Campus, Bebek, Istanbul, Turkey.
| | - Elif Merve Eminoğlu
- Faculty of Arts and Sciences, Department of Chemistry, Marmara University, 34722 Göztepe, Istanbul, Turkey
| | - Safiye Sağ Erdem
- Faculty of Arts and Sciences, Department of Chemistry, Marmara University, 34722 Göztepe, Istanbul, Turkey
| | - Marjana Novič
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
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Tripathi PN, Srivastava P, Sharma P, Seth A, Shrivastava SK. Design and development of novel N-(pyrimidin-2-yl)-1,3,4-oxadiazole hybrids to treat cognitive dysfunctions. Bioorg Med Chem 2019; 27:1327-1340. [PMID: 30795991 DOI: 10.1016/j.bmc.2019.02.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/25/2022]
Abstract
Novel hybrids bearing a 2-aminopyrimidine (2-AP) moiety linked to substituted 1,3,4-oxadiazoles were designed, synthesized and biologically evaluated. Among the developed compounds, 28 noncompetitively inhibited human acetylcholinesterase (hAChE; pIC50 = 6.52; Ki = 0.17 µM) and showed potential in vitro antioxidant activity (60.0%) when evaluated using the Ellman's and DPPH assays, respectively. Compound 28 competitively displaced propidium iodide (PI) from the peripheral anionic site (PAS) of hAChE (17.6%) and showed high blood-brain barrier (BBB) permeability, as observed in the PAMPA-BBB assay. Additionally, compound 28 inhibited hAChE-induced Aβ aggregation in a concentration-dependent manner according to the thioflavin T assay and was devoid of neurotoxic liability towards SH-SY5Y cell lines, as demonstrated by the MTT assay. The behavioral studies of compound 28 in mice showed a significant reversal of scopolamine-induced amnesia, as observed in Y-maze and passive avoidance tests. Furthermore, compound 28 exhibited significant AChE inhibition in the brain in ex vivo studies. An evaluation of oxidative stress biomarkers revealed the antioxidant potential of 28. Moreover, in silico molecular docking and dynamics simulation studies were used as a computational tool to evaluate the interactions of compound 28 with the active site residues of hAChE.
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Affiliation(s)
- Prabhash Nath Tripathi
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221 005, India
| | - Pavan Srivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221 005, India
| | - Piyoosh Sharma
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221 005, India
| | - Ankit Seth
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221 005, India
| | - Sushant K Shrivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221 005, India.
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15
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Veeraragavulu P, Yellapu NK, Yerrathota S, Adi PJ, Matcha B. Three Novel Mutations I65S, R66S, and G86R Divulge Significant Conformational Variations in the PTB Domain of the IRS1 Gene. ACS OMEGA 2019; 4:2217-2224. [PMID: 31660472 PMCID: PMC6814177 DOI: 10.1021/acsomega.8b01712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/25/2018] [Indexed: 06/10/2023]
Abstract
Insulin receptor substrate 1 (IRS1) is one of the major substrates for the IR, and their interaction mediates several downstream insulin signaling pathways. In this study, we have identified three novel mutations in the IRS1 gene of type 2 diabetic (T2D) patients, which reflected in the amino acid changes as I65S, R66S, and G86R in the phosphotyrosine binding domain of the IRS1 protein. The impact of these mutations on the structure and function of the IRS1 protein was evaluated through molecular modeling studies, and distinct conformational fluctuations were recorded. The variable binding affinities and positional displacement of these mutant models were observed in the ligand-binding cleft of IR. The mutant IRS1 models triggered conformational changes in the L1 domain of IR upon their binding. Such structural variations in IRS1 and IR structures due to mutations resulted in variable molecular interactions that could lead to altered insulin transduction, followed by insulin resistance and T2D.
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Affiliation(s)
| | - Nanda Kumar Yellapu
- Division
of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati 517502, India
| | - Sireesha Yerrathota
- Division
of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati 517502, India
| | - Pradeepkiran Jangampalli Adi
- Division
of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati 517502, India
- Garrison
Institute on Aging, Texas Tech University
Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, Texas 79430, United
States
| | - Bhaskar Matcha
- Division
of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati 517502, India
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16
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Fonseca TG, Auguste M, Ribeiro F, Cardoso C, Mestre NC, Abessa DMS, Bebianno MJ. Environmental relevant levels of the cytotoxic drug cyclophosphamide produce harmful effects in the polychaete Nereis diversicolor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 636:798-809. [PMID: 29727846 DOI: 10.1016/j.scitotenv.2018.04.318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 06/08/2023]
Abstract
Cytotoxic drugs applied in chemotherapy enter the aquatic environment after patient's metabolism and excretion, in both main compounds and their respective metabolites. The increased consumption and discharge of these drugs raise concern on the genotoxic burden to non-target aquatic species, due to their unselective action on DNA. Settlement and adsorption of cytotoxic drugs to aquatic sediments pose risks to benthic species through chronic exposure. The aim of the present study was to assess the effects induced by the anticancer drug cyclophosphamide (CP) on the polychaete Nereis diversicolor, after 14 days of exposure to environmental relevant concentrations (10, 100, 500 and 1000 ng L-1). Burrowing impairment, neurotoxicity (Acetylcholinesterase - AChE activity), oxidative stress (superoxide dismutase - SOD; catalase - CAT; glutathione peroxidases - GPXs activities), biotransformation (glutathione-S-transferases - GST), oxidative damage (lipid peroxidation - LPO) and genotoxicity (DNA damage) were assessed. Burrowing impairments were higher at the lowest CP concentrations tested. The higher CP levels tested (500 and 1000 ng L-1) induced a significant inhibition on the enzymatic antioxidant system (SOD, GPx) and on GST activity. DNA damage was also significant at these concentrations as an outcome of CP metabolism, and high levels of oxidative damage occurred. The results showed that the prodrug CP was metabolically activated in the benthic biological model N. diversicolor. In addition to the potential cytotoxic impact likely to be caused in aquatic species with similar metabolism, N. diversicolor proved to be reliable and vulnerable to the cytotoxic mode of action of CP, even at the lower doses.
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Affiliation(s)
- T G Fonseca
- CIMA, Centre for Marine and Environmental Research, University of Algarve, Campus Gambelas, 8005-135 Faro, Portugal; NEPEA, Núcleo de Estudos em Poluição e Ecotoxicologia. Aquática, Universidade Estadual Paulista - UNESP, Campus Experimental do Litoral Paulista, Praça Infante Dom Henrique, s/n, 11330-900 São Vicente, SP, Brazil
| | - M Auguste
- CIMA, Centre for Marine and Environmental Research, University of Algarve, Campus Gambelas, 8005-135 Faro, Portugal
| | - F Ribeiro
- CIMA, Centre for Marine and Environmental Research, University of Algarve, Campus Gambelas, 8005-135 Faro, Portugal
| | - C Cardoso
- CIMA, Centre for Marine and Environmental Research, University of Algarve, Campus Gambelas, 8005-135 Faro, Portugal
| | - N C Mestre
- CIMA, Centre for Marine and Environmental Research, University of Algarve, Campus Gambelas, 8005-135 Faro, Portugal
| | - D M S Abessa
- NEPEA, Núcleo de Estudos em Poluição e Ecotoxicologia. Aquática, Universidade Estadual Paulista - UNESP, Campus Experimental do Litoral Paulista, Praça Infante Dom Henrique, s/n, 11330-900 São Vicente, SP, Brazil
| | - M J Bebianno
- CIMA, Centre for Marine and Environmental Research, University of Algarve, Campus Gambelas, 8005-135 Faro, Portugal.
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17
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Kalani K, Yan SF, Yan SS. Mitochondrial permeability transition pore: a potential drug target for neurodegeneration. Drug Discov Today 2018; 23:1983-1989. [PMID: 30081095 PMCID: PMC6449145 DOI: 10.1016/j.drudis.2018.08.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 07/17/2018] [Accepted: 08/01/2018] [Indexed: 12/21/2022]
Abstract
The mitochondrial permeability transition pore (mPTP) has been considered a key contributor to cell death, inducing the process in several major neurodegenerative diseases. To date, the molecular nature of the mPTP remains confounding but its significance is universally acknowledged. Several targets have been screened and inhibition of mPTP has emerged as an attractive field for researchers. Nowadays, in silico-directed studies help to explore new small molecules targeting the mPTP to improve their drug-like properties and bioactivity. Here, we briefly summarize the role of mPTP in neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson disease (PD), and Huntington's disease (HD), and discusses current and future potential therapeutic targets.
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Affiliation(s)
- Komal Kalani
- Department of Pharmacology and Toxicology, Higuchi Bioscience Center, School of Pharmacy, University of Kansas, Lawrence, KS 66047, USA
| | - Shi Fang Yan
- Department of Pharmacology and Toxicology, Higuchi Bioscience Center, School of Pharmacy, University of Kansas, Lawrence, KS 66047, USA
| | - Shirley ShiDu Yan
- Department of Pharmacology and Toxicology, Higuchi Bioscience Center, School of Pharmacy, University of Kansas, Lawrence, KS 66047, USA.
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18
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Kuruva CS, Gandavaram SP, Kadiam VS, Valluru L, Chamarthi NR. Synthesis of New Heteroaryl α‐Aminophosphonates and Evaluation of Their Cytotoxicity against Human Breast Cancer MCF‐7 Cell Lines. ChemistrySelect 2018. [DOI: 10.1002/slct.201800700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Chandra S. Kuruva
- Department of ChemistrySri Venkateswara University Tirupati 517502 India
| | - Syam P. Gandavaram
- Department of ChemistrySree Vidyanikethan Engineering College, Sree Sainath Nagar Tirupati 517102 India
| | | | | | - Naga R. Chamarthi
- Department of ChemistrySri Venkateswara University Tirupati 517502 India
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19
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Zhu Y, Han Y, Ma Y, Yang P. ADME/toxicity prediction and antitumor activity of novel nitrogenous heterocyclic compounds designed by computer targeting of alkylglycerone phosphate synthase. Oncol Lett 2018; 16:1431-1438. [PMID: 30008821 PMCID: PMC6036461 DOI: 10.3892/ol.2018.8873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 02/15/2018] [Indexed: 12/24/2022] Open
Abstract
Alkylglycerone phosphate synthase (AGPS) is an oncogene and can be considered as an antitumor drug target. The aim of the present study was to design novel nitrogenous heterocyclic compound improving targetability by computer-aided drug design technology targeting AGPS. A total of 12 nitrogenous heterocyclic compounds were designed and predicted the absorption, distribution, metabolism and excretion parameters/toxicity. Their activity in terms of proliferation inhibition, cell cycle arrest and apoptosis induction was then measured using an MTS assay and a high-content screening system in U251 cells. The results showed that anti-glioma activity was present in compounds N4, N5, N6, N7, N8 and N12, which was in accordance with the computer prediction. Therefore, these compounds may be suitable for the development of a novel glioma therapeutic drug.
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Affiliation(s)
- Yu Zhu
- Department of Clinical Laboratory, Tianjin Key Laboratory of Cerebral Vessels and Neural Degeneration, Tianjin Huanhu Hospital, Tianjin 300350, P.R. China
| | - Yuan Han
- Department of Clinical Laboratory, Tianjin Key Laboratory of Cerebral Vessels and Neural Degeneration, Tianjin Huanhu Hospital, Tianjin 300350, P.R. China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Ping Yang
- Department of Clinical Laboratory, Tianjin Key Laboratory of Cerebral Vessels and Neural Degeneration, Tianjin Huanhu Hospital, Tianjin 300350, P.R. China
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20
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Yang B, Li X, He L, Zhu Y. Computer-aided design of temozolomide derivatives based on alkylglycerone phosphate synthase structure with isothiocyanate and their pharmacokinetic/toxicity prediction and anti-tumor activity in vitro. Biomed Rep 2018; 8:235-240. [PMID: 29599977 PMCID: PMC5867473 DOI: 10.3892/br.2018.1051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/25/2017] [Indexed: 12/18/2022] Open
Abstract
Despite the development of temozolomide (TMZ), a novel type of glioma therapeutic drug, malignant glioma remains to cause severe damage to human health. The present study aimed to utilize the molecular biological differences between tumor and normal cells to design TMZ derivatives with improved selectivity and targeting using computer-aided drug design (CADD). Taking alkylglycerone phosphate synthase (AGPS) as a target, a 3D structure-activity relationship model was built using CADD technology; molecular docking of isothiocyanate (ITC) and TMZ compounds was conducted; ITC-TMZ derivatives were designed; and predictions on the absorption, distribution, metabolism and excretion (ADME) processes and toxicity of the ITC-TMZ derivatives were established in order to obtain improved understanding of the structure-activity relationship of the candidate compounds. Using these techniques, it was identified that the docking scores of the structural derivatives S1-9 were higher than that of TMZ. Additionally, S3, −6, −7, −8, −9 and −10 exhibited enhanced ADME and similar toxicity to that of TMZ. The half maximal inhibitory concentrations of the CADD derivatives were also assessed in the glioma U87MG and U251 cell lines, and the activities of S1, −3, −8 and −10 were determined to be greater than that of TMZ, suggesting their potential as anti-cancer drugs with adequate AGPS targeting, ADME/toxicity and anti-tumor activity.
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Affiliation(s)
- Bing Yang
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Xiaobo Li
- Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Lu He
- Department of Anatomy and Histology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Yu Zhu
- Department of Clinical Laboratory, Tianjin Key Laboratory of Cerebral Vessels and Neural Degeneration, Tianjin Huanhu Hospital, Tianjin 300350, P.R. China
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21
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Kumar J, Gill A, Shaikh M, Singh A, Shandilya A, Jameel E, Sharma N, Mrinal N, Hoda N, Jayaram B. Pyrimidine-Triazolopyrimidine and Pyrimidine-Pyridine Hybrids as Potential Acetylcholinesterase Inhibitors for Alzheimer's Disease. ChemistrySelect 2018. [DOI: 10.1002/slct.201702599] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jitendra Kumar
- Department of Chemistry; Jamia Millia Islamia (Central University); New Delhi- 110025 India
| | - Asim Gill
- Laboratory of Molecular Biology; South Asian University; New Delhi- 110021 India
| | - Marziya Shaikh
- Laboratory of Molecular Biology; South Asian University; New Delhi- 110021 India
| | - Anju Singh
- Department of Chemistry; Jamia Millia Islamia (Central University); New Delhi- 110025 India
| | - Ashutosh Shandilya
- Department of Chemistry; Indian Institute of Technology Delhi, Hauz Khas; New Delhi- 110016 India
| | - Ehtesham Jameel
- Department of Chemistry; Jamia Millia Islamia (Central University); New Delhi- 110025 India
| | - Nitin Sharma
- Laboratory of Molecular Biology; South Asian University; New Delhi- 110021 India
| | - Nirotpal Mrinal
- Laboratory of Molecular Biology; South Asian University; New Delhi- 110021 India
| | - Nasimul Hoda
- Department of Chemistry; Jamia Millia Islamia (Central University); New Delhi- 110025 India
| | - B. Jayaram
- Department of Chemistry; Indian Institute of Technology Delhi, Hauz Khas; New Delhi- 110016 India
- Kusuma School of Biological Sciences; IIT Delhi; New Delhi- 110016 India
- Supercomputing facility for Bioinformatics & Computational Biology; IIT Delhi; New Delhi- 110016 India
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22
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Metformin and Its Sulfenamide Prodrugs Inhibit Human Cholinesterase Activity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:7303096. [PMID: 28770024 PMCID: PMC5523189 DOI: 10.1155/2017/7303096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 06/05/2017] [Accepted: 06/14/2017] [Indexed: 01/29/2023]
Abstract
The results of epidemiological and pathophysiological studies suggest that type 2 diabetes mellitus (T2DM) may predispose to Alzheimer's disease (AD). The two conditions present similar glucose levels, insulin resistance, and biochemical etiologies such as inflammation and oxidative stress. The diabetic state also contributes to increased acetylcholinesterase (AChE) activity, which is one of the factors leading to neurodegeneration in AD. The aim of this study was to assess in vitro the effects of metformin, phenformin, and metformin sulfenamide prodrugs on the activity of human AChE and butyrylcholinesterase (BuChE) and establish the type of inhibition. Metformin inhibited 50% of the AChE activity at micromolar concentrations (2.35 μmol/mL, mixed type of inhibition) and seemed to be selective towards AChE since it presented low anti-BuChE activity. The tested metformin prodrugs inhibited cholinesterases (ChE) at nanomolar range and thus were more active than metformin or phenformin. The cyclohexyl sulfenamide prodrug demonstrated the highest activity towards both AChE (IC50 = 890 nmol/mL, noncompetitive inhibition) and BuChE (IC50 = 28 nmol/mL, mixed type inhibition), while the octyl sulfenamide prodrug did not present anti-AChE activity, but exhibited mixed inhibition towards BuChE (IC50 = 184 nmol/mL). Therefore, these two bulkier prodrugs were concluded to be the most selective compounds for BuChE over AChE. In conclusion, it was demonstrated that biguanides present a novel class of inhibitors for AChE and BuChE and encourages further studies of these compounds for developing both selective and nonselective inhibitors of ChEs in the future.
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23
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Hossain T, Saha A, Mukherjee A. Exploring molecular structural requirement for AChE inhibition through multi-chemometric and dynamics simulation analyses. J Biomol Struct Dyn 2017; 36:1274-1285. [DOI: 10.1080/07391102.2017.1320231] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Tabassum Hossain
- Department of Chemical Technology, University of Calcutta, 92, A. P. C. Road, Kolkata, 700009, India
| | - Achintya Saha
- Department of Chemical Technology, University of Calcutta, 92, A. P. C. Road, Kolkata, 700009, India
| | - Arup Mukherjee
- Department of Chemical Technology, University of Calcutta, 92, A. P. C. Road, Kolkata, 700009, India
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24
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Ismaili L, Refouvelet B, Benchekroun M, Brogi S, Brindisi M, Gemma S, Campiani G, Filipic S, Agbaba D, Esteban G, Unzeta M, Nikolic K, Butini S, Marco-Contelles J. Multitarget compounds bearing tacrine- and donepezil-like structural and functional motifs for the potential treatment of Alzheimer's disease. Prog Neurobiol 2017; 151:4-34. [DOI: 10.1016/j.pneurobio.2015.12.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 11/11/2015] [Accepted: 12/11/2015] [Indexed: 01/16/2023]
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25
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Synthesis and Structure of 7-Hydroxy-5-Oxo-2,3-Dihydro-5H-[1,3]Thiazolo[3,2-a]-Pyrimidine-6-Carboxylic Acid Ethyl Ester. Pharm Chem J 2017. [DOI: 10.1007/s11094-017-1557-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Zhang A, Mu Y, Wu F. An enantiomer-based virtual screening approach: Discovery of chiral organophosphates as acetyl cholinesterase inhibitors. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 138:215-222. [PMID: 28061415 DOI: 10.1016/j.ecoenv.2016.12.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/23/2016] [Accepted: 12/27/2016] [Indexed: 06/06/2023]
Abstract
Chiral organophosphates (OPs) have been used widely around the world, very little is known about binding mechanisms with biological macromolecules. An in-depth understanding of the stereo selectivity of human AChE and discovering bioactive enantiomers of OPs can decrease health risks of these chiral chemicals. In the present study, a flexible molecular docking approach was conducted to investigate different binding modes of twelve phosphorus enantiomers. A pharmacophore model was then developed on basis of the bioactive conformations of these compounds. After virtual screening, twenty-four potential bioactive compounds were found, of which three compounds (Ethyl p-nitrophenyl phenylphosphonate (EPN), 1-naphthaleneacetic anhydride and N,4-dimethyl-N-phenyl-benzenesulfonamide) were tested by use of different in vitro assays. S-isomer of EPN was also found to exhibit greater inhibitory activity towards human AChE than the corresponding R-isomer. These findings affirm that stereochemistry plays a crucial role in virtual screening, and provide a new insight into designing safer organ phosphorus pesticides on human health.
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Affiliation(s)
- Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yunsong Mu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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27
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Ahmad S, Iftikhar F, Ullah F, Sadiq A, Rashid U. Rational design and synthesis of dihydropyrimidine based dual binding site acetylcholinesterase inhibitors. Bioorg Chem 2016; 69:91-101. [DOI: 10.1016/j.bioorg.2016.10.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/06/2016] [Accepted: 10/08/2016] [Indexed: 01/26/2023]
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28
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Gurung AB, Aguan K, Mitra S, Bhattacharjee A. Identification of molecular descriptors for design of novel Isoalloxazine derivatives as potential Acetylcholinesterase inhibitors against Alzheimer's disease. J Biomol Struct Dyn 2016; 35:1729-1742. [PMID: 27410776 DOI: 10.1080/07391102.2016.1192485] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In Alzheimer's disease (AD), the level of Acetylcholine (ACh) neurotransmitter is reduced. Since Acetylcholinesterase (AChE) cleaves ACh, inhibitors of AChE are very much sought after for AD treatment. The side effects of current inhibitors necessitate development of newer AChE inhibitors. Isoalloxazine derivatives have proved to be promising (AChE) inhibitors. However, their structure-activity relationship studies have not been reported till date. In the present work, various quantitative structure-activity relationship (QSAR) building methods such as multiple linear regression (MLR), partial least squares ,and principal component regression were employed to derive 3D-QSAR models using steric and electrostatic field descriptors. Statistically significant model was obtained using MLR coupled with stepwise selection method having r2 = .9405, cross validated r2 (q2) = .6683, and a high predictability (pred_r2 = .6206 and standard error, pred_r2se = .2491). Steric and electrostatic contribution plot revealed three electrostatic fields E_496, E_386 and E_577 and one steric field S_60 contributing towards biological activity. A ligand-based 3D-pharmacophore model was generated consisting of eight pharmacophore features. Isoalloxazine derivatives were docked against human AChE, which revealed critical residues implicated in hydrogen bonds as well as hydrophobic interactions. The binding modes of docked complexes (AChE_IA1 and AChE_IA14) were validated by molecular dynamics simulation which showed their stable trajectories in terms of root mean square deviation and molecular mechanics/Poisson-Boltzmann surface area binding free energy analysis revealed key residues contributing significantly to overall binding energy. The present study may be useful in the design of more potent Isoalloxazine derivatives as AChE inhibitors.
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Affiliation(s)
- Arun Bahadur Gurung
- a Computational Biology Laboratory, Department of Biotechnology and Bioinformatics , North-Eastern Hill University , Shillong 793022 , India
| | - Kripamoy Aguan
- b Molecular Biology Laboratory, Department of Biotechnology and Bioinformatics , North-Eastern Hill University , Shillong 793022 , India
| | - Sivaprasad Mitra
- c Center for Advanced Studies in Chemistry , North-Eastern Hill University , Shillong 793022 , India
| | - Atanu Bhattacharjee
- a Computational Biology Laboratory, Department of Biotechnology and Bioinformatics , North-Eastern Hill University , Shillong 793022 , India
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29
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Ochoa R, Rodriguez CA, Zuluaga AF. Perspectives for the structure-based design of acetylcholinesterase reactivators. J Mol Graph Model 2016; 68:176-183. [PMID: 27450771 DOI: 10.1016/j.jmgm.2016.07.002] [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: 02/23/2016] [Revised: 05/31/2016] [Accepted: 07/17/2016] [Indexed: 02/03/2023]
Abstract
Rational design of active molecules through structure-based methods has been gaining adepts during the last decades due to the wider availability of protein structures, most of them conjugated with relevant ligands. Acetylcholinesterase (AChE) is a molecular target with a considerable amount of data related to its sequence and 3-dimensional structure. In addition, there are structural insights about the mechanism of action of the natural substrate and drugs used in Alzheimer's disease, organophosphorus compounds, among others. We looked for AChE structural data useful for in silico design of potential interacting molecules. In particular, we focused on information regarding the design of ligands aimed to reactivate AChE catalytic activity. The structures of 178 AChE were annotated and categorized on different subsets according to the nature of the ligand, source organisms and experimental details. We compared sequence homology among the active site from Torpedo californica, Mus musculus and Homo sapiens with the latter two species having the closest relationship (88.9% identity). In addition, the mechanism of organophosphorus binding and the design of effective reactivators are reviewed. A curated data collection obtained with information from several sources was included for researchers working on the field. Finally, a molecular dynamics simulation with human AChE indicated that the catalytic pocket volume stabilizes around 600 Å(3), providing additional clues for drug design.
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Affiliation(s)
- Rodrigo Ochoa
- CIEMTO: Centro de Información y Estudio de Medicamentos y Tóxicos, Departamento de Farmacología y Toxicología, Facultad de Medicina, Universidad de Antioquia, Carrera 51D No. 62-42 Medellín, Colombia.
| | - Carlos A Rodriguez
- CIEMTO: Centro de Información y Estudio de Medicamentos y Tóxicos, Departamento de Farmacología y Toxicología, Facultad de Medicina, Universidad de Antioquia, Carrera 51D No. 62-42 Medellín, Colombia; GRIPE: Grupo Investigador de Problemas en Enfermedades Infecciosas, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
| | - Andres F Zuluaga
- CIEMTO: Centro de Información y Estudio de Medicamentos y Tóxicos, Departamento de Farmacología y Toxicología, Facultad de Medicina, Universidad de Antioquia, Carrera 51D No. 62-42 Medellín, Colombia; GRIPE: Grupo Investigador de Problemas en Enfermedades Infecciosas, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
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Molecular Docking Study on Galantamine Derivatives as Cholinesterase Inhibitors. Mol Inform 2015; 34:394-403. [DOI: 10.1002/minf.201400145] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/08/2014] [Indexed: 01/14/2023]
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Vangavaragu JR, Valasani KR, Fang D, Williams TD, Yan SS. Determination of small molecule ABAD inhibitors crossing blood-brain barrier and pharmacokinetics. J Alzheimers Dis 2015; 42:333-44. [PMID: 24858403 DOI: 10.3233/jad-140252] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A major obstacle to the development of effective treatment of Alzheimer's disease (AD) is successfully delivery of drugs to the brain. We have previously identified a series of benzothiazole phosphonate compounds that block the interaction of amyloid-β peptide with amyloid-β binding alcohol dehydrogenase (ABAD). A selective and sensitive method for the presence of three new benzothiazole ABAD inhibitors in mouse plasma, brain, and artificial cerebrospinal fluid has been developed and validated based on high performance liquid chromatography tandem mass spectrometry. Mass spectra were generated using Micromass Quattro Ultima "triple" quadrupole mass spectrometer equipped with an Electrospray Ionization interface. Good linearity was obtained over a concentration range of 0.05-2.5 μg/ml. The lowest limit of quantification and detection was found to be 0.05 μg/ml. All inter-day accuracies and precisions were within ± 15% of the nominal value and ± 20%, respectively, at the lower limit of quantitation. The tested compounds were stable at various conditions with recoveries >90.0% (RSD <10%). The method used for pharmacokinetic studies of compounds in mouse cerebrospinal fluid, plasma, and brain is accurate, precise, and specific with no matrix effect. Pharmacokinetic data showed that these compounds penetrate the blood-brain barrier (BBB) yielding 4-50 ng/ml peak brain concentrations and 2 μg/ml peak plasma concentrations from a 10 mg/kg dose. These results indicate that our newly synthesized small molecule ABAD inhibitors have a good drug properties with the ability to cross the blood-brain barrier, which holds a great potential for AD therapy.
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Affiliation(s)
- Jhansi Rani Vangavaragu
- Department of Pharmacology & Toxicology, Higuchi Bioscience Center, School of Pharmacy, University of Kansas, Lawrence, KS, USA
| | - Koteswara Rao Valasani
- Department of Pharmacology & Toxicology, Higuchi Bioscience Center, School of Pharmacy, University of Kansas, Lawrence, KS, USA
| | - Du Fang
- Department of Pharmacology & Toxicology, Higuchi Bioscience Center, School of Pharmacy, University of Kansas, Lawrence, KS, USA
| | - Todd D Williams
- Mass Spectrometry Laboratory University of Kansas, Lawrence, KS, USA
| | - Shirley ShiDu Yan
- Department of Pharmacology & Toxicology, Higuchi Bioscience Center, School of Pharmacy, University of Kansas, Lawrence, KS, USA
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Sekhar KC, Syed R, Golla M, Kumar M V J, Yellapu NK, Chippada AR, Chamarthi NR. Novel heteroaryl phosphonicdiamides PTPs inhibitors as anti-hyperglycemic agents. Daru 2014; 22:76. [PMID: 25542373 PMCID: PMC4305230 DOI: 10.1186/s40199-014-0076-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 11/13/2014] [Indexed: 11/05/2023] Open
Abstract
BACKGROUND Chronic and oral administration of benzylamine improves glucose tolerance. Picolylamine is a selective functional antagonist of the human adenosine A2B receptor. Phosphonic diamide derivatives enhance the cellular permeability and in turn their biological activities. METHODS A series of heteroaryl phosphonicdiamide derivatives were designed as therapeutics to control and manage type2 diabetes. Initially defined Lipinski parameters encouraged them as safer drugs. Molecular docking of these compounds against Protein tyrosine phosphatase (PTP), the potential therapeutic target of type 2 diabetes, revealed their potential binding ability explaining their anti-diabetic activity in terms of PTP inhibition. Human intestinal absorption, Caco-2 cell permeability, MDCK cell permeability, BBB penetration, skin permeability and plasma protein binding abilities of the title compounds were calculated by PreADMET server. A convenient method has been developed for the synthesis of title compounds through the formation of 1-ethoxy-N,N'-bis(4-fluorobenzyl/pyridin-3-ylmethyl)phosphinediamine by the reaction of 4-fluorobenzylamine/ 3-picolylamine with ethyldichlorophosphite, subsequently reacted with heteroaryl halides using lanthanum(III) chloride as a catalyst. RESULTS All the compounds exhibited significant in vitro anti-oxidant activity and in vivo evaluation in streptozotocin induced diabetic rat models revealed that the normal glycemic levels were observed on 12(th) day by 9a and 20(th) day by 5b, 5c, 9e and 9f. The remaining compounds also exhibited normal glycemic levels by 25(th) day. CONCLUSION The results from molecular modeling, in vitro and in vivo studies are suggesting them as safer and effective therapeutic agents against type2 diabetes. Graphical Abstract Development of PTPs inhibitors.
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Affiliation(s)
| | - Rasheed Syed
- Department of Chemistry, Sri Venkateswara University, Tirupati, 517 502, India.
| | - Madhava Golla
- Department of Chemistry, Sri Venkateswara University, Tirupati, 517 502, India.
| | - Jyothi Kumar M V
- Department of Biotechnology, Sri Venkateswara University, Tirupati, 517 502, India.
| | - Nanda Kumar Yellapu
- Biomedical informatics Center, Vector Control Research Centre, Indian Council of Medical Research, Puducherry, 605006, India.
| | - Appa Rao Chippada
- Department of Biochemistry, Sri Venkateswara University, Tirupati, 517 502, India.
| | - Naga Raju Chamarthi
- Department of Chemistry, Sri Venkateswara University, Tirupati, 517 502, India.
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Kilaru RB, Valasani KR, Yellapu NK, Osuru HP, Kuruva CS, Matcha B, Chamarthi NR. Design, synthesis, in silico and in vitro studies of novel 4-methylthiazole-5-carboxylic acid derivatives as potent anti-cancer agents. Bioorg Med Chem Lett 2014; 24:4580-4585. [DOI: 10.1016/j.bmcl.2014.07.058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 07/07/2014] [Accepted: 07/21/2014] [Indexed: 11/29/2022]
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Rao VK, Carlson EA, Yan SS. Mitochondrial permeability transition pore is a potential drug target for neurodegeneration. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1842:1267-72. [PMID: 24055979 PMCID: PMC3991756 DOI: 10.1016/j.bbadis.2013.09.003] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 09/07/2013] [Indexed: 01/16/2023]
Abstract
Mitochondrial permeability transition pore (mPTP) plays a central role in alterations of mitochondrial structure and function leading to neuronal injury relevant to aging and neurodegenerative diseases including Alzheimer's disease (AD). mPTP putatively consists of the voltage-dependent anion channel (VDAC), the adenine nucleotide translocator (ANT) and cyclophilin D (CypD). Reactive oxygen species (ROS) increase intra-cellular calcium and enhance the formation of mPTP that leads to neuronal cell death in AD. CypD-dependent mPTP can play a crucial role in ischemia/reperfusion injury. The interaction of amyloid beta peptide (Aβ) with CypD potentiates mitochondrial and neuronal perturbation. This interaction triggers the formation of mPTP, resulting in decreased mitochondrial membrane potential, impaired mitochondrial respiration function, increased oxidative stress, release of cytochrome c, and impaired axonal mitochondrial transport. Thus, the CypD-dependent mPTP is directly linked to the cellular and synaptic perturbations observed in the pathogenesis of AD. Designing small molecules to block this interaction would lessen the effects of Aβ neurotoxicity. This review summarizes the recent progress on mPTP and its potential therapeutic target for neurodegenerative diseases including AD.
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Affiliation(s)
- Valasani Koteswara Rao
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS 66047, USA
| | - Emily A Carlson
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS 66047, USA
| | - Shirley Shidu Yan
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS 66047, USA.
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Gupta S, Mohan CG. Dual binding site and selective acetylcholinesterase inhibitors derived from integrated pharmacophore models and sequential virtual screening. BIOMED RESEARCH INTERNATIONAL 2014; 2014:291214. [PMID: 25050335 PMCID: PMC4094703 DOI: 10.1155/2014/291214] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 04/08/2014] [Indexed: 11/28/2022]
Abstract
In this study, we have employed in silico methodology combining double pharmacophore based screening, molecular docking, and ADME/T filtering to identify dual binding site acetylcholinesterase inhibitors that can preferentially inhibit acetylcholinesterase and simultaneously inhibit the butyrylcholinesterase also but in the lesser extent than acetylcholinesterase. 3D-pharmacophore models of AChE and BuChE enzyme inhibitors have been developed from xanthostigmine derivatives through HypoGen and validated using test set, Fischer's randomization technique. The best acetylcholinesterase and butyrylcholinesterase inhibitors pharmacophore hypotheses Hypo1_A and Hypo1_B, with high correlation coefficient of 0.96 and 0.94, respectively, were used as 3D query for screening the Zinc database. The screened hits were then subjected to the ADME/T and molecular docking study to prioritise the compounds. Finally, 18 compounds were identified as potential leads against AChE enzyme, showing good predicted activities and promising ADME/T properties.
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Affiliation(s)
- Shikhar Gupta
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S.Nagar, Punjab 160 062, India
| | - C. Gopi Mohan
- Amrita Centre for Nanosciences and Molecular Medicine (ACNSMM), Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham University, Ponekkara, Kochi, Kerala State 682 041, India
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Valasani KR, Carlson EA, Battaile KP, Bisson A, Wang C, Lovell S, Yan SS. High-resolution crystal structures of two crystal forms of human cyclophilin D in complex with PEG 400 molecules. Acta Crystallogr F Struct Biol Commun 2014; 70:717-22. [PMID: 24915078 PMCID: PMC4051522 DOI: 10.1107/s2053230x14009480] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/28/2014] [Indexed: 11/10/2022] Open
Abstract
Cyclophilin D (CypD) is a key mitochondrial target for amyloid-β-induced mitochondrial and synaptic dysfunction and is considered a potential drug target for Alzheimer's disease. The high-resolution crystal structures of primitive orthorhombic (CypD-o) and primitive tetragonal (CypD-t) forms have been determined to 1.45 and 0.85 Å resolution, respectively, and are nearly identical structurally. Although an isomorphous structure of CypD-t has previously been reported, the structure reported here was determined at atomic resolution, while CypD-o represents a new crystal form for this protein. In addition, each crystal form contains a PEG 400 molecule bound to the same region along with a second PEG 400 site in CypD-t which occupies the cyclosporine A inhibitor binding site of CypD. Highly precise structural information for CypD should be extremely useful for discerning the detailed interaction of small molecules, particularly drugs and/or inhibitors, bound to CypD. The 0.85 Å resolution structure of CypD-t is the highest to date for any CypD structure.
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Affiliation(s)
- Koteswara Rao Valasani
- Department of Pharmacology and Toxicology and Higuchi Bioscience Center, University of Kansas, Lawrence, KS 66047, USA
| | - Emily A. Carlson
- Department of Pharmacology and Toxicology and Higuchi Bioscience Center, University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P. Battaile
- IMCA-CAT, Hauptman–Woodward Medical Research Institute, 9700 South Cass Avenue, Building 435A, Argonne, IL 60439, USA
| | - Andrea Bisson
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS 66047, USA
| | - Shirley ShiDu Yan
- Department of Pharmacology and Toxicology and Higuchi Bioscience Center, University of Kansas, Lawrence, KS 66047, USA
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Yellapu N, Mahto MK, Valasani KR, Sarma P, Matcha B. Mutations in exons 10 and 11 of human glucokinase result in conformational variations in the active site of the structure contributing to poor substrate binding – explains hyperglycemia in type 2 diabetic patients. J Biomol Struct Dyn 2014; 33:820-33. [DOI: 10.1080/07391102.2014.913989] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Nandakumar Yellapu
- Division of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati, Andhrapradesh 517502, India
- Biomedical Informatics Center, Vector Control Research Center, Indian Council of Medical Research, Pondicherry, 605006 India
| | - Manoj Kumar Mahto
- Division of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati, Andhrapradesh 517502, India
| | - Koteswara Rao Valasani
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS, 66047 USA
| | - P.V.G.K. Sarma
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhrapradesh, 517507 India
| | - Bhaskar Matcha
- Division of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati, Andhrapradesh 517502, India
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Valasani K, Vangavaragu JR, Day VW, Yan SS. Structure based design, synthesis, pharmacophore modeling, virtual screening, and molecular docking studies for identification of novel cyclophilin D inhibitors. J Chem Inf Model 2014; 54:902-12. [PMID: 24555519 PMCID: PMC3985759 DOI: 10.1021/ci5000196] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Indexed: 11/29/2022]
Abstract
Cyclophilin D (CypD) is a peptidyl prolyl isomerase F that resides in the mitochondrial matrix and associates with the inner mitochondrial membrane during the mitochondrial membrane permeability transition. CypD plays a central role in opening the mitochondrial membrane permeability transition pore (mPTP) leading to cell death and has been linked to Alzheimer's disease (AD). Because CypD interacts with amyloid beta (Aβ) to exacerbate mitochondrial and neuronal stress, it is a potential target for drugs to treat AD. Since appropriately designed small organic molecules might bind to CypD and block its interaction with Aβ, 20 trial compounds were designed using known procedures that started with fundamental pyrimidine and sulfonamide scaffolds know to have useful therapeutic effects. Two-dimensional (2D) quantitative structure-activity relationship (QSAR) methods were applied to 40 compounds with known IC50 values. These formed a training set and were followed by a trial set of 20 designed compounds. A correlation analysis was carried out comparing the statistics of the measured IC50 with predicted values for both sets. Selectivity-determining descriptors were interpreted graphically in terms of principle component analyses. These descriptors can be very useful for predicting activity enhancement for lead compounds. A 3D pharmacophore model was also created. Molecular dynamics simulations were carried out for the 20 trial compounds with known IC50 values, and molecular descriptors were determined by 2D QSAR studies using the Lipinski rule-of-five. Fifteen of the 20 molecules satisfied all 5 Lipinski rules, and the remaining 5 satisfied 4 of the 5 Lipinski criteria and nearly satisfied the fifth. Our previous use of 2D QSAR, 3D pharmacophore models, and molecular docking experiments to successfully predict activity indicates that this can be a very powerful technique for screening large numbers of new compounds as active drug candidates. These studies will hopefully provide a basis for efficiently designing and screening large numbers of more potent and selective inhibitors for CypD treatment of AD.
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Affiliation(s)
- Koteswara
Rao Valasani
- Department
of Pharmacology & Toxicology and Higuchi Bioscience Center, School
of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
| | - Jhansi Rani Vangavaragu
- Department
of Pharmacology & Toxicology and Higuchi Bioscience Center, School
of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
| | - Victor W. Day
- Department
of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Shirley ShiDu Yan
- Department
of Pharmacology & Toxicology and Higuchi Bioscience Center, School
of Pharmacy, University of Kansas, Lawrence, Kansas 66047, United States
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39
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Prasad UV, Swarupa V, Yeswanth S, Kumar PS, Kumar ES, Reddy KMK, Kumar YN, Rani VJ, Chaudhary A, Sarma PVGK. Structural and Functional analysis of Staphylococcus aureus NADP-dependent IDH and its comparison with Bacterial and Human NADPdependent IDH. Bioinformation 2014; 10:81-6. [PMID: 24616559 PMCID: PMC3937580 DOI: 10.6026/97320630010081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 01/31/2014] [Indexed: 01/14/2023] Open
Abstract
Staphylococcus aureus a natural inhabitant of nasopharyngeal tract mainly survives as biofilms and possess complete Krebs cycle which plays major role in its pathogenesis. This TCA cycle is regulated by Isocitrate dehydrogenase (IDH) we have earlier cloned, sequenced (HM067707), expressed and characterized this enzyme from S. aureus ATCC12600. We have observed only one type of IDH in all the strains of S. aureus which dictates the flow of carbon thereby controlling the virulence and biofilm formation, this phenomenon is variable among bacteria. Therefore in the present study comparative structural and functional analysis of IDH was undertaken. As the crystal structure of S. aureus IDH was not available therefore using the deduced amino sequence of complete gene the 3D structure of IDH was built in Modeller 9v8. The PROCHECK and ProSAweb analysis showed the built structure was close to the crystal structure of Bacillus subtilis. This structure when superimposed with other bacterial IDH structures exhibited extensive structural variations as evidenced from the RMSD values correlating with extensive sequential variations. Only 24% sequence identity was observed with both human NADP dependent IDHs (PDB: 1T09 and 1T0L) and the structural comparative studies indicated extensive structural variations with an RMSD values of 14.284Å and 10.073Å respectively. Docking of isocitrate to both human IDHs and S. aureus IDH structures showed docking scores of -11.6169 and -10.973 respectively clearly indicating higher binding affinity of isocitrate to human IDH.
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Affiliation(s)
- Uppu Venkateswara Prasad
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, India, 517507
| | - Vimjam Swarupa
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, India, 517507
| | - Sthanikam Yeswanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, India, 517507
| | - Pasupuleti Santhosh Kumar
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, India, 517507
| | - Easambadi Siva Kumar
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, AP, India, 517507
| | | | - Yellapu Nanda Kumar
- Department of Zoology, Sri Venkateswara University, Tirupati, AP, India, 517502
| | | | - Abhijit Chaudhary
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati - 517 507
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Vangavaragu JR, Valasani KR, Gan X, Yan SS. Identification of human presequence protease (hPreP) agonists for the treatment of Alzheimer's disease. Eur J Med Chem 2014; 76:506-16. [PMID: 24602793 DOI: 10.1016/j.ejmech.2014.02.046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 02/11/2014] [Accepted: 02/16/2014] [Indexed: 01/08/2023]
Abstract
Amyloid-β (Aβ), a neurotoxic peptide, is linked to the onset of Alzheimer's disease (AD). Increased Aβ content within neuronal cell mitochondria is a pathological feature in both human and mouse models with AD. This accumulation of Aβ within the mitochondrial landscape perpetuates increased free radical production and activation of the apoptotic pathway. Human Presequence Protease (hPreP) is responsible for the degradation of mitochondrial amyloid-β peptide in human neuronal cells, and is thus an attractive target to increase the proteolysis of Aβ. Therefore, it offers a potential target for Alzheimer's drug design, by identifying potential activators of hPreP. We applied structure-based drug design, combined with experimental methodologies to investigate the ability of various compounds to enhance hPreP proteolytic activity. Compounds 3c &4c enhanced hPreP-mediated proteolysis of Aβ (1-42), pF₁β (2-54) and fluorogenic-substrate V. These results suggest that activation of hPreP by small benzimidazole derivatives provide a promising avenue for AD treatment.
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Affiliation(s)
- Jhansi Rani Vangavaragu
- Department of Pharmacology and Toxicology, and Higuchi Bioscience Center, School of Pharmacy, University of Kansas, 2099 Constant Ave., Lawrence, KS 66047, USA
| | - Koteswara Rao Valasani
- Department of Pharmacology and Toxicology, and Higuchi Bioscience Center, School of Pharmacy, University of Kansas, 2099 Constant Ave., Lawrence, KS 66047, USA
| | - Xueqi Gan
- Department of Pharmacology and Toxicology, and Higuchi Bioscience Center, School of Pharmacy, University of Kansas, 2099 Constant Ave., Lawrence, KS 66047, USA
| | - Shirley ShiDu Yan
- Department of Pharmacology and Toxicology, and Higuchi Bioscience Center, School of Pharmacy, University of Kansas, 2099 Constant Ave., Lawrence, KS 66047, USA.
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Cacabelos R, Cacabelos P, Torrellas C, Tellado I, Carril JC. Pharmacogenomics of Alzheimer's disease: novel therapeutic strategies for drug development. Methods Mol Biol 2014; 1175:323-556. [PMID: 25150875 DOI: 10.1007/978-1-4939-0956-8_13] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Alzheimer's disease (AD) is a major problem of health and disability, with a relevant economic impact on our society. Despite important advances in pathogenesis, diagnosis, and treatment, its primary causes still remain elusive, accurate biomarkers are not well characterized, and the available pharmacological treatments are not cost-effective. As a complex disorder, AD is a polygenic and multifactorial clinical entity in which hundreds of defective genes distributed across the human genome may contribute to its pathogenesis. Diverse environmental factors, cerebrovascular dysfunction, and epigenetic phenomena, together with structural and functional genomic dysfunctions, lead to amyloid deposition, neurofibrillary tangle formation, and premature neuronal death, the major neuropathological hallmarks of AD. Future perspectives for the global management of AD predict that genomics and proteomics may help in the search for reliable biomarkers. In practical terms, the therapeutic response to conventional drugs (cholinesterase inhibitors, multifactorial strategies) is genotype-specific. Genomic factors potentially involved in AD pharmacogenomics include at least five categories of gene clusters: (1) genes associated with disease pathogenesis; (2) genes associated with the mechanism of action of drugs; (3) genes associated with drug metabolism (phase I and II reactions); (4) genes associated with drug transporters; and (5) pleiotropic genes involved in multifaceted cascades and metabolic reactions. The implementation of pharmacogenomic strategies will contribute to optimize drug development and therapeutics in AD and related disorders.
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Affiliation(s)
- Ramón Cacabelos
- Chair of Genomic Medicine, Camilo José Cela University, 28692, Villanueva de la Cañada, Madrid, Spain,
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