1
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Kumar Tiwari P, Chouhan M, Mishra R, Gupta S, Chaudhary AA, Al-Zharani M, Ahmed Qurtam A, Nasr FA, Jha NK, Pant K, Kumar M, Kumar S. Structure-based virtual screening methods for the identification of novel phytochemical inhibitors targeting furin protease for the management of COVID-19. Front Cell Infect Microbiol 2024; 14:1391288. [PMID: 38919703 PMCID: PMC11196402 DOI: 10.3389/fcimb.2024.1391288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 04/29/2024] [Indexed: 06/27/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, is a highly contagious respiratory disease with widespread societal impact. The symptoms range from cough, fever, and pneumonia to complications affecting various organs, including the heart, kidneys, and nervous system. Despite various ongoing efforts, no effective drug has been developed to stop the spread of the virus. Although various types of medications used to treat bacterial and viral diseases have previously been employed to treat COVID-19 patients, their side effects have also been observed. The way SARS-CoV-2 infects the human body is very specific, as its spike protein plays an important role. The S subunit of virus spike protein cleaved by human proteases, such as furin protein, is an initial and important step for its internalization into a human host. Keeping this context, we attempted to inhibit the furin using phytochemicals that could produce minimal side effects. For this, we screened 408 natural phytochemicals from various plants having antiviral properties, against furin protein, and molecular docking and dynamics simulations were performed. Based on the binding score, the top three compounds (robustaflavone, withanolide, and amentoflavone) were selected for further validation. MM/GBSA energy calculations revealed that withanolide has the lowest binding energy of -57.2 kcal/mol followed by robustaflavone and amentoflavone with a binding energy of -45.2 kcal/mol and -39.68 kcal/mol, respectively. Additionally, ADME analysis showed drug-like properties for these three lead compounds. Hence, these natural compounds robustaflavone, withanolide, and amentoflavone, may have therapeutic potential for the management of SARS-CoV-2 by targeting furin.
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Affiliation(s)
- Prashant Kumar Tiwari
- Biological and Bio-computational Lab, Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Mandeep Chouhan
- Biological and Bio-computational Lab, Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Richa Mishra
- Department of Computer Engineering, Parul University, Gujarat, India
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Mohammed Al-Zharani
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Ashraf Ahmed Qurtam
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Fahd A. Nasr
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Niraj Kumar Jha
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
- School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, India
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Kumud Pant
- Department of Biotechnology, Graphic Era Deemed to Be University, Dehradun, Uttarakhand, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjay Kumar
- Biological and Bio-computational Lab, Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
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2
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Kumar M, Dubey R, Kumar Shukla P, Dayal D, Kumar Chaubey K, Tsai LW, Kumar S. Identification of small molecule inhibitors of RAD52 for breast cancer therapy: in silico approach. J Biomol Struct Dyn 2024; 42:4605-4618. [PMID: 37288783 DOI: 10.1080/07391102.2023.2220822] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/29/2023] [Indexed: 06/09/2023]
Abstract
The breast cancer susceptibility gene 1/2 (BRCA1/2) are the key regulators in maintaining the genomic integrity and mutations in these genes have been associated with development of breast and ovarian cancers. Also, synthetic lethality has been shown in BRCA1/2 deficient cancers, when the RAD52 gene is silenced by shRNA or small molecules aptamers, suggesting a role for RAD52 in the breast cancers pathogenesis. Thus, to find the potential inhibitors of RAD52, a collection of 21,000 compounds from the ChemBridge screening library was screened to conduct molecular docking and molecular dynamics simulation (MD) against RAD52. Further, the results were validated by a density functional theory (DFT) analysis and using post-dynamics free energy calculations. Out of all screened molecules, the docking study revealed five compounds were found to have promising activities against RAD52. Moreover, the catalytic amino acid residues of RAD52 developed stable contacts with compound 8758 and 10593, as anticipated by DFT calculation, MD simulation, and post dynamics MM-GBSA energy calculation. It appears that compound 8758 is the best inhibitor against RAD52 followed by 10593 compared to the other top hits, in terms of the HOMO orbital energy (-1.0966 eV and -1.2136 eV) from DFT and the post dynamics binding free energy calculation (-54.71 and -52.43 Kcal/mol). Furthermore, a drug-like properties of lead molecules (8758 and 10593) were also seen via ADMET analysis. Based on our computational analysis, we hypothesize that a small molecule 8758 and 10593 possess the therapeutic potential in the management for breast cancer patients with a BRCA mutation via targeting RAD52.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mukesh Kumar
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Rajni Dubey
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Prakash Kumar Shukla
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Deen Dayal
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
| | - Kundan Kumar Chaubey
- Division of Research and Innovation, School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Lung-Wen Tsai
- Department of Medicine Research, Taipei Medical University Hospital, Taipei, Taiwan
- Department of Information Technology Office, Taipei Medical University Hospital, Taipei, Taiwan
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei, Taiwan
| | - Sanjay Kumar
- Biological and Bio-computational Lab, Department of Life Sciences, Sharda School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India
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3
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Lotfi B, Mebarka O, Alhatlani BY, Abdallah EM, Kawsar SMA. Pharmacoinformatics and Breed-Based De Novo Hybridization Studies to Develop New Neuraminidase Inhibitors as Potential Anti-Influenza Agents. Molecules 2023; 28:6678. [PMID: 37764457 PMCID: PMC10534564 DOI: 10.3390/molecules28186678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/09/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza represents a profoundly transmissible viral ailment primarily afflicting the respiratory system. Neuraminidase inhibitors constitute a class of antiviral therapeutics employed in the management of influenza. These inhibitors impede the liberation of the viral neuraminidase protein, thereby impeding viral dissemination from the infected cell to host cells. As such, neuraminidase has emerged as a pivotal target for mitigating influenza and its associated complications. Here, we apply a de novo hybridization approach based on a breed-centric methodology to elucidate novel neuraminidase inhibitors. The breed technique amalgamates established ligand frameworks with the shared target, neuraminidase, resulting in innovative inhibitor constructs. Molecular docking analysis revealed that the seven synthesized breed molecules (designated Breeds 1-7) formed more robust complexes with the neuraminidase receptor than conventional clinical neuraminidase inhibitors such as zanamivir, oseltamivir, and peramivir. Pharmacokinetic evaluations of the seven breed molecules (Breeds 1-7) demonstrated favorable bioavailability and optimal permeability, all falling within the specified parameters for human application. Molecular dynamics simulations spanning 100 nanoseconds corroborated the stability of these breed molecules within the active site of neuraminidase, shedding light on their structural dynamics. Binding energy assessments, which were conducted through MM-PBSA analysis, substantiated the enduring complexes formed by the seven types of molecules and the neuraminidase receptor. Last, the investigation employed a reaction-based enumeration technique to ascertain the synthetic pathways for the synthesis of the seven breed molecules.
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Affiliation(s)
- Bourougaa Lotfi
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, BP 145, Biskra 70700, Algeria;
| | - Ouassaf Mebarka
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, BP 145, Biskra 70700, Algeria;
| | - Bader Y. Alhatlani
- Unit of Scientific Research, Applied College, Qassim University, Buraydah 52571, Saudi Arabia
| | - Emad M. Abdallah
- Department of Science Laboratories, College of Science and Arts, Qassim University, Ar Rass 51921, Saudi Arabia;
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh;
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Kumari R, Singhvi N, Sharma P, Choudhury C, Shakya R. Virtual screening of gut microbiome bacteriocins as potential inhibitors of stearoyl-CoA desaturase 1 to regulate adipocyte differentiation and thermogenesis to combat obesity. J Biomol Struct Dyn 2023; 41:12632-12642. [PMID: 36644882 DOI: 10.1080/07391102.2023.2167121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
The gut bacterial strains and their metabolites have been shown to play a significant role in obesity, but the molecular mechanisms underlying this association are largely unresolved. Obesity is a multifactorial problem and is controlled by various mechanisms and pathways to produce and store fat cells. Bacteriocins are secondary metabolites produced by gut bacteria to defend themselves against their competitors. Recently, they have gained great attention due to their role in metabolic disorders, including obesity. Stearoyl-CoA desaturase 1 (SCD1) is a key enzyme involved in the differentiation of adipocytes. The aim of this study is to show the regulation of SCD1 by bacteriocins and thus their importance in obesity control. We screened the human gut bacteriome for the presence of bacteriocins, predicted their structures, and showed their inhibitory role by molecular docking with SCD1. Further, to confirm the docking results, MDS of six top scoring SCD1-bacteriocin complexes were carried out for 100 ns. These six bacteriocins namely, Plantaricin S-beta, Carnolysin, Lactococcin B, Bacteriocin Iic, Plantaricin N, and Thermophilin A, with strong binding affinities, are primarily produced by bacterial strains from the Lactobacillaeacea family. These findings can be the basis of further experiments for enhanced understanding of the underlying mechanisms for obesity control, specifically bacteriocins driven regulation of the SCD1 enzyme. In addition, a consortium of bacterial strains producing these bacteriocins can be developed and used as probiotics for the amelioration of obesity and other metabolic complications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rekha Kumari
- Molecular Microbiology and Bioinformatics Laboratory, Department of Zoology, Miranda House, University of Delhi, Delhi, India
| | - Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, Uttarakhand, India
| | - Poonam Sharma
- Department of Zoology, Gargi College, University of Delhi, Delhi, India
| | - Chinmayee Choudhury
- Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh, India
| | - Rashmi Shakya
- Department of Botany, Miranda House, University of Delhi, Delhi, India
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5
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Wang N, Liu W, Zhou L, Liu W, Liang X, Liu X, Xu Z, Zhong T, Wu Q, Jiao X, Chen J, Ning X, Jiang X, Zhao Q. Design, Synthesis, and Biological Evaluation of Notopterol Derivatives as Triple Inhibitors of AChE/BACE1/GSK3β for the Treatment of Alzheimer's Disease. ACS OMEGA 2022; 7:32131-32152. [PMID: 36120034 PMCID: PMC9476211 DOI: 10.1021/acsomega.2c03368] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
The pathogenesis of Alzheimer's disease (AD) is very complex, and there are many hypotheses. Therefore, the development of a multi-target-directed-ligand may be an effective therapeutic strategy. Our previous study showed that notopterol (a natural product from Notopterygium) is a dual BACE1/GSK3β inhibitor. In this study, we designed and synthesized 48 notopterol derivatives with furacoumarin as a scaffold in order to enhance their balanced AChE/BACE1/GSK3β inhibitory activity. Fortunately, 1c showed effective inhibitory activity against AChE (58.7% at 1.0 μM), BACE1 (48.3% at 20 μM), and GSK3β (40.3% at 10 μM). Furthermore, 1c showed good blood-brain barrier penetrability, suitable bioavailability, and oral safety. More importantly, 1c could ameliorate the impaired learning and memory in Aβ-induced AD mice. In conclusion, we reported the triple inhibitor of AChE/BACE1/GSK3β lead compounds based on a furocoumarin scaffold of notopterol for the first time, which provides a potential new strategy for the treatment of AD.
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Affiliation(s)
- Nan Wang
- Department
of Pharmacy, General Hospital of Northern
Theater Command, Shenyang110840, People’s Republic
of China
- School
of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang110016, People’s Republic of China
| | - Wenjie Liu
- School
of Traditional Chinese Materia Medica, Shenyang
Pharmaceutical University, Shenyang110016, People’s Republic
of China
| | - Lijun Zhou
- School
of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang110016, People’s Republic of China
| | - Wenwu Liu
- School
of Traditional Chinese Materia Medica, Shenyang
Pharmaceutical University, Shenyang110016, People’s Republic
of China
| | - Xu Liang
- School
of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang110016, People’s Republic of China
| | - Xin Liu
- School
of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang110016, People’s Republic of China
| | - Zihua Xu
- Department
of Pharmacy, General Hospital of Northern
Theater Command, Shenyang110840, People’s Republic
of China
| | - Tianming Zhong
- Department
of Pharmacy, General Hospital of Northern
Theater Command, Shenyang110840, People’s Republic
of China
| | - Qiong Wu
- Department
of Pharmacy, General Hospital of Northern
Theater Command, Shenyang110840, People’s Republic
of China
| | - Xinming Jiao
- School
of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang110016, People’s Republic of China
| | - Jiangxia Chen
- School
of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang110016, People’s Republic of China
| | - Xinyue Ning
- School
of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang110016, People’s Republic of China
| | - Xiaowen Jiang
- Department
of Pharmacy, General Hospital of Northern
Theater Command, Shenyang110840, People’s Republic
of China
- School
of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang110016, People’s Republic of China
- Key
Laboratory of Structure-Based Drug Design & Discovery, Ministry
of Education, Shenyang Pharmaceutical University, Shenyang110016, People’s Republic of China
| | - Qingchun Zhao
- Department
of Pharmacy, General Hospital of Northern
Theater Command, Shenyang110840, People’s Republic
of China
- School
of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang110016, People’s Republic of China
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6
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Tripathi MK, Singh P, Kumar M, Sharma K, Singh TP, Ethayathulla AS, Kaur P. Identification of a promising inhibitor from Illicium verum (star anise) against the main protease of SARS-CoV-2: insights from the computational study. J Biomol Struct Dyn 2022:1-17. [PMID: 35980746 DOI: 10.1080/07391102.2022.2112621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
SARS-CoV-2, the causing agent of coronavirus disease (COVID-19), first broke out in Wuhan and rapidly spread worldwide, resulting in a global health emergency. The lack of specific drugs against the coronavirus has made its spread challenging to control. The main protease (Mpro) is a key enzyme of SARS-CoV-2 used as a key target in drug discovery against the coronavirus. Medicines derived from plant phytoconstituents have been widely exploited to treat various diseases. The present study has evaluated the potential of Illicium verum (star anise) phytoconstituents against Mpro by implementing a computational approach. We performed molecular docking and molecular dynamics simulation study with a set of 60 compounds to identify their potential to inhibit the main protease (Mpro) of SARS-CoV-2. DFT study and post dynamics free energy calculations were also performed to strengthen the findings. The identified four compounds by docking study exhibited the highest potential compared to other selected phytoconstituents. Further, density functional theory (DFT) calculation, molecular dynamics simulation and post dynamics MM-GBSA energy calculation predicted Verimol-G as a potential compound, which formed stable interactions through the catalytic dyad residues. The HOMO orbital energy (-0.250038) from DFT and the post dynamics binding free energy calculation (-73.33 Kcal/mol) correlate, suggesting Verimol-G is the best inhibitor compared to the other phytoconstituents. This compound also complies with the ADME properties of drug likeliness. Thus, based on a computational study, we suggest that Verimol G may be developed as a potential inhibitor against the main protease to combat COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Pushpendra Singh
- State Virus Research and Diagnostic Laboratory, Department of Microbiology, All India Institute of Medical Sciences, Raipur, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Kuldeep Sharma
- State Virus Research and Diagnostic Laboratory, Department of Microbiology, All India Institute of Medical Sciences, Raipur, India
| | - T P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - A S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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7
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Deng L, Viray K, Singh S, Cravatt B, Stella N. ABHD6 Controls Amphetamine-Stimulated Hyperlocomotion: Involvement of CB 1 Receptors. Cannabis Cannabinoid Res 2021; 7:188-198. [PMID: 34705543 PMCID: PMC9070749 DOI: 10.1089/can.2021.0066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Introduction: Activation of cannabinoid 1 receptors (CB1Rs) by endocannabinoids (eCBs) is controlled by both eCB production and eCB inactivation. Accordingly, inhibition of eCB hydrolyzing enzymes, monoacylglycerol lipase (MAGL) and α/β-hydrolase domain containing 6 (ABHD6), enhances eCB accumulation and CB1R activation. It is known that inhibition of MAGL regulates select CB1R-dependent behaviors in mice, including locomotor behaviors and their modulation by psychostimulants, but much less is known about the effect of inhibiting ABHD6 activity on such behaviors. Methods: We report a new mouse line that carries a genetic deletion of Abhd6 and evaluated its effect on spontaneous locomotion measured in a home cage monitoring system, motor coordination measured on a Rotarod, and amphetamine-stimulated hyperlocomotion and amphetamine sensitization (AS) measured in an open-field chamber. Results: ABHD6 knockout (KO) mice reached adulthood without exhibiting overt behavioral impairment, and we measured only mild reduction in spontaneous locomotion and motor coordination in adult ABHD6 KO mice compared to wild-type (WT) mice. Significantly, amphetamine-stimulated hyperlocomotion was enhanced by twofold in ABHD6 KO mice compared to WT mice and yet ABHD6 KO mice expressed AS to the same extent as WT mice. A twofold increase in amphetamine-stimulated hyperlocomotion was also measured in ABHD6 heterozygote mice and in WT mice treated with the ABHD6 inhibitor KT-182. It is known that amphetamine-stimulated hyperlocomotion is not affected by the CB1R antagonist, SR141617, and we discovered that the enhanced amphetamine-stimulated hyperlocomotion resulting from ABHD6 inhibition is blocked by SR141617. Conclusions: Our study suggests that ABHD6 controls amphetamine-stimulated hyperlocomotion by a mechanistic switch to a CB1R-dependent mechanism.
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Affiliation(s)
- Liting Deng
- Department of Pharmacology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Katie Viray
- Department of Pharmacology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Simar Singh
- Department of Pharmacology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Ben Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
| | - Nephi Stella
- Department of Pharmacology, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington, USA
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8
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Singh P, Tripathi MK, Yasir M, Khare R, Shrivastava R. In silico identification of promising inhibitor against RNA-dependent RNA polymerase target of SARS-CoV-2. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2021; 10:131-140. [PMID: 34476266 PMCID: PMC8340315 DOI: 10.22099/mbrc.2021.40367.1621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The severe acute respiratory syndrome is a viral respiratory disease recognised as COVID-19, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Formerly, no precise remedies are available, and many studies regarding COVID-19 prevention and treatment are under development. Several targets for the design of drugs are identified, and studies are in headway to explore the potential target. RNA-dependent RNA polymerase (RdRp) protein identified as a promising target against SARS-CoV-2 infection for the drug design due to its significant role in viral replication. The present study focuses on identifying the binding effect of previously known RdRp inhibitors with RdRp of SARS-CoV-2 using molecular docking and molecular dynamics simulation approaches. Molecular docking and binding free energy calculations against RdRp enzyme identified suramin as a potential compound that showed the highest docking score of -7.83 Kcal/mole and binding energy of -80.83 Kcal/mole as a comparison to other compounds. Further, molecular dynamics simulation studies were moreover showed the stable binding behaviour of suramin docked complex in the protein active site. Thus, the study concludes that suramin might be helpful as a potential inhibitor against RNA-dependent RNA polymerase of SRAS-CoV-2. However, further investigation is needed to assess the possible effect of inhibitors on RdRp through in vitro and in vivo experiments.
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Affiliation(s)
- Pushpendra Singh
- State Virus Research and Diagnostic Laboratory, Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh-492099 India.,Equally contributed, Pushpendra Singh and Manish Kumar Tripathi both are joint first author
| | - Manish Kumar Tripathi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India.,Equally contributed, Pushpendra Singh and Manish Kumar Tripathi both are joint first author
| | - Mohammad Yasir
- Department of Nephrology, All India Institute of Medical Science Bhopal, Madhya Pradesh-462020 India
| | - Ruchi Khare
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh-462003 India
| | - Rahul Shrivastava
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh-462003 India
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9
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Cao JK, Viray K, Shin M, Hsu KL, Mackie K, Westenbroek R, Stella N. ABHD6 Inhibition Rescues a Sex-Dependent Deficit in Motor Coordination in The HdhQ200/200 Mouse Model of Huntington's Disease. JOURNAL OF NEUROLOGY AND NEUROLOGICAL DISORDERS 2021; 7:106. [PMID: 37720694 PMCID: PMC10503675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Huntington's Disease is associated with motor behavior deficits that are lessened by few therapeutic options. This preliminary study tested if pharmacological inhibition of α/β-hydrolase domain containing 6 (ABHD6), a multifunctional enzyme expressed in the striatum, rescues behavioral deficits in HdhQ200/200 mice. Previous work has shown that this model exhibits a reduction in spontaneous locomotion and motor coordination at 8 and 10 months of age, with a more severe phenotype in female mice. Semi-quantitative immunohistochemistry analysis indicated no change in striatal ABHD6 expression at 8 months of age, but a 40% reduction by 10 months in female HdhQ200/200 mice compared to female wild-type (WT) littermates. At 8 months of age, acute ABHD6 inhibition rescued motor coordination deficits in female HdhQ200/200 mice without affecting WT performance. ABHD6 inhibition did not impact spontaneous locomotion, grip strength, or overall weight in either group, showing that effects were specific to motor coordination. At 10 months of age, semi-chronic ABHD6 inhibition by osmotic pump delivery also rescued motor coordination deficits in female HdhQ200/200 mice without affecting female WT littermates. Our preliminary study suggests that ABHD6 inhibition improves motor performance in female HdhQ200/200 mice.
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Affiliation(s)
- JK Cao
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - K Viray
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - M Shin
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - K-L Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - K Mackie
- Department of Psychological and Brain Sciences, Linda and Jack Gill Center for Biomolecular Science, Indiana University, Bloomington, IN 47405, USA
| | - R Westenbroek
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - N Stella
- Department of Pharmacology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
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10
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Bononi G, Tuccinardi T, Rizzolio F, Granchi C. α/β-Hydrolase Domain (ABHD) Inhibitors as New Potential Therapeutic Options against Lipid-Related Diseases. J Med Chem 2021; 64:9759-9785. [PMID: 34213320 PMCID: PMC8389839 DOI: 10.1021/acs.jmedchem.1c00624] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Much of the experimental evidence in the literature has linked altered lipid metabolism to severe diseases such as cancer, obesity, cardiovascular pathologies, diabetes, and neurodegenerative diseases. Therefore, targeting key effectors of the dysregulated lipid metabolism may represent an effective strategy to counteract these pathological conditions. In this context, α/β-hydrolase domain (ABHD) enzymes represent an important and diversified family of proteins, which are involved in the complex environment of lipid signaling, metabolism, and regulation. Moreover, some members of the ABHD family play an important role in the endocannabinoid system, being designated to terminate the signaling of the key endocannabinoid regulator 2-arachidonoylglycerol. This Perspective summarizes the research progress in the development of ABHD inhibitors and modulators: design strategies, structure-activity relationships, action mechanisms, and biological studies of the main ABHD ligands will be highlighted.
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Affiliation(s)
- Giulia Bononi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Flavio Rizzolio
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy.,Department of Molecular Sciences and Nanosystems, Ca' Foscari University, 30123 Venezia, Italy
| | - Carlotta Granchi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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11
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Zięba A, Laitinen T, Patel JZ, Poso A, Kaczor AA. Docking-Based 3D-QSAR Studies for 1,3,4-oxadiazol-2-one Derivatives as FAAH Inhibitors. Int J Mol Sci 2021; 22:6108. [PMID: 34204026 PMCID: PMC8201265 DOI: 10.3390/ijms22116108] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 11/16/2022] Open
Abstract
This work aimed to construct 3D-QSAR CoMFA and CoMSIA models for a series of 31 FAAH inhibitors, containing the 1,3,4-oxadiazol-2-one moiety. The obtained models were characterized by good statistical parameters: CoMFA Q2 = 0.61, R2 = 0.98; CoMSIA Q2 = 0.64, R2 = 0.93. The CoMFA model field contributions were 54.1% and 45.9% for steric and electrostatic fields, respectively. In the CoMSIA model, electrostatic, steric, hydrogen bond donor, and hydrogen acceptor properties were equal to 34.6%, 23.9%, 23.4%, and 18.0%, respectively. These models were validated by applying the leave-one-out technique, the seven-element test set (CoMFA r2test-set = 0.91; CoMSIA r2test-set = 0.91), a progressive scrambling test, and external validation criteria developed by Golbraikh and Tropsha (CoMFA r20 = 0.98, k = 0.95; CoMSIA r20 = 0.98, k = 0.89). As the statistical significance of the obtained model was confirmed, the results of the CoMFA and CoMSIA field calculation were mapped onto the enzyme binding site. It gave us the opportunity to discuss the structure-activity relationship based on the ligand-enzyme interactions. In particular, examination of the electrostatic properties of the established CoMFA model revealed fields that correspond to the regions where electropositive substituents are not desired, e.g., in the neighborhood of the 1,3,4-oxadiazol-2-one moiety. This highlights the importance of heterocycle, a highly electronegative moiety in this area of each ligand. Examination of hydrogen bond donor and acceptor properties contour maps revealed several spots where the implementation of another hydrogen-bond-donating moiety will positively impact molecules' binding affinity, e.g., in the neighborhood of the 1,3,4-oxadiazol-2-one ring. On the other hand, there is a large isopleth that refers to the favorable H-bond properties close to the terminal phenoxy group of a ligand, which means that, generally speaking, H-bond acceptors are desired in this area.
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Affiliation(s)
- Agata Zięba
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, PL-20059 Lublin, Poland
| | - Tuomo Laitinen
- School of Pharmacy, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Jayendra Z Patel
- Division of Pharmaceutical Chemistry and Technology, University of Helsinki, FI-00790 Helsinki, Finland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, FI-70211 Kuopio, Finland
- Department of Internal Medicine VIII, University Hospital Tübingen, DE-72076 Tübingen, Germany
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, PL-20059 Lublin, Poland
- School of Pharmacy, University of Eastern Finland, FI-70211 Kuopio, Finland
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12
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Sivakumar D, Stein M. Binding of SARS-CoV Covalent Non-Covalent Inhibitors to the SARS-CoV-2 Papain-Like Protease and Ovarian Tumor Domain Deubiquitinases. Biomolecules 2021; 11:biom11060802. [PMID: 34071582 PMCID: PMC8227062 DOI: 10.3390/biom11060802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 12/23/2022] Open
Abstract
The urgent need for novel and effective drugs against the SARS-CoV-2 coronavirus pandemic has stimulated research worldwide. The Papain-like protease (PLpro), which is essential for viral replication, shares a similar active site structural architecture to other cysteine proteases. Here, we have used representatives of the Ovarian Tumor Domain deubiquitinase family OTUB1 and OTUB2 along with the PLpro of SARS-CoV-2 to validate and rationalize the binding of inhibitors from previous SARS-CoV candidate compounds. By forming a new chemical bond with the cysteine residue of the catalytic triad, covalent inhibitors irreversibly suppress the protein’s activity. Modeling covalent inhibitor binding requires detailed knowledge about the compounds’ reactivities and binding. Molecular Dynamics refinement simulations of top poses reveal detailed ligand-protein interactions and show their stability over time. The recently discovered selective OTUB2 covalent inhibitors were used to establish and validate the computational protocol. Structural parameters and ligand dynamics are in excellent agreement with the ligand-bound OTUB2 crystal structures. For SARS-CoV-2 PLpro, recent covalent peptidomimetic inhibitors were simulated and reveal that the ligand-protein interaction is very dynamic. The covalent and non-covalent docking plus subsequent MD refinement of known SARS-CoV inhibitors into DUBs and the SARS-CoV-2 PLpro point out a possible approach to target the PLpro cysteine protease from SARS-CoV-2. The results show that such an approach gives insight into ligand-protein interactions, their dynamic character, and indicates a path for selective ligand design.
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13
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Tripathi MK, Singh P, Sharma S, Singh TP, Ethayathulla AS, Kaur P. Identification of bioactive molecule from Withania somnifera (Ashwagandha) as SARS-CoV-2 main protease inhibitor. J Biomol Struct Dyn 2020; 39:5668-5681. [PMID: 32643552 PMCID: PMC7441797 DOI: 10.1080/07391102.2020.1790425] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 is the causative agent of COVID-19 and has been declared as pandemic disease by World Health Organization. Lack of targeted therapeutics and vaccines for COVID-2019 have triggered the scientific community to develop new vaccines or drugs against this novel virus. Many synthetic compounds and antimalarial drugs are undergoing clinical trials. The traditional medical practitioners widely use Indian medicinal plant Withania somnifera (Ashwagandha) natural constituents, called withanolides for curing various diseases. The main protease (Mpro) of SARS-CoV-2 plays a vital role in disease propagation by processing the polyproteins which are required for its replication. Hence, it denotes a significant target for drug discovery. In the present study, we evaluate the potential of 40 natural chemical constituents of Ashwagandha to explore a possible inhibitor against main protease of SARS-CoV-2 by adopting the computational approach. The docking study revealed that four constituents of Ashwagandha; Withanoside II (-11.30 Kcal/mol), Withanoside IV (-11.02 Kcal/mol), Withanoside V (-8.96 Kcal/mol) and Sitoindoside IX (-8.37 Kcal/mol) exhibited the highest docking energy among the selected natural constituents. Further, MD simulation study of 100 ns predicts Withanoside V possess strong binding affinity and hydrogen-bonding interactions with the protein active site and indicates its stability in the active site. The binding free energy score also correlates with the highest score of -87.01 ± 5.01 Kcal/mol as compared to other selected compounds. In conclusion, our study suggests that Withanoside V in Ashwagandha may be serve as a potential inhibitor against Mpro of SARS-CoV-2 to combat COVID-19 and may have an antiviral effect on nCoV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Pushpendra Singh
- ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - A S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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14
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Pan Z, Wang Y, Gu X, Wang J, Cheng M. Refined homology model of cytochrome bcc complex B subunit for virtual screening of potential anti-tuberculosis agents. J Biomol Struct Dyn 2019; 38:4733-4745. [DOI: 10.1080/07391102.2019.1688196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Zhenhai Pan
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning, P. R. China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Ying Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Xi Gu
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning, P. R. China
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, P. R. China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning, P. R. China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning, P. R. China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, P. R. China
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15
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The Universal 3D QSAR Model for Dopamine D 2 Receptor Antagonists. Int J Mol Sci 2019; 20:ijms20184555. [PMID: 31540025 PMCID: PMC6770028 DOI: 10.3390/ijms20184555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/06/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022] Open
Abstract
In order to search for novel antipsychotics acting through the D2 receptor, it is necessary to know the structure–activity relationships for dopamine D2 receptor antagonists. In this context, we constructed the universal three-dimensional quantitative structure–activity relationship (3D- QSAR) model for competitive dopamine D2 receptor antagonists. We took 176 compounds from chemically different groups characterized by the half maximal inhibitory concentration (IC50)from the CHEMBL database and docked them to the X-ray structure of the human D2 receptor in the inactive state. Selected docking poses were applied for Comparative Molecular Field Analysis (CoMFA) alignment. The obtained CoMFA model is characterized by a cross-validated coefficient Q2 of 0.76 with an optimal component of 5, R2 of 0.92, and an F value of 338.9. The steric and electrostatic field contributions are 67.4% and 32.6%, respectively. The statistics obtained prove that the CoMFA model is significant. Next, the IC50 of the 16 compounds from the test set was predicted with R2 of 0.95. Finally, a progressive scrambling test was carried out for additional validation. The CoMFA fields were mapped onto the dopamine D2 receptor binding site, which enabled a discussion of the structure–activity relationship based on ligand–receptor interactions. In particular, it was found that one of the desired steric interactions covers the area of a putative common allosteric pocket suggested for some other G protein-coupled receptors (GPCRs), which would suggest that some of the known dopamine receptor antagonists are bitopic in their essence. The CoMFA model can be applied to predict the potential activity of novel dopamine D2 receptor antagonists.
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16
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Hu B, Zheng X, Wang Y, Wang J, Zhang F. Computational Approaches for Elucidating Protein-Protein Interactions in Cation Channel Signaling. Curr Drug Targets 2019; 21:179-192. [PMID: 31490747 DOI: 10.2174/1389450120666190906154412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/10/2019] [Accepted: 08/23/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The lipid bilayer of the plasma membrane is impermeable to ions, yet changes in the flux of ions across the cell membrane are critical regulatory events in cells. Because of their regulatory roles in a range of physiological processes, such as electrical signaling in muscles and neurons, to name a few, these proteins are one of the most important drug targets. OBJECTIVE This review mainly focused on the computational approaches for elucidating proteinprotein interactions in cation channel signaling. DISCUSSION Due to continuously advanced facilities and technologies in computer sciences, the physical contacts of macromolecules of channel structures have been virtually visualized. Indeed, techniques like protein-protein docking, homology modeling, and molecular dynamics simulation are valuable tools for predicting the protein complex and refining channels with unreleased structures. Undoubtedly, these approaches will greatly expand the cation channel signaling research, thereby speeding up structure-based drug design and discovery. CONCLUSION We introduced a series of valuable computational tools for elucidating protein-protein interactions in cation channel signaling, including molecular graphics, protein-protein docking, homology modeling, and molecular dynamics simulation.
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Affiliation(s)
- Baichun Hu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Xiaoming Zheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Ying Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China.,Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China.,School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Fengjiao Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
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17
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Cao JK, Kaplan J, Stella N. ABHD6: Its Place in Endocannabinoid Signaling and Beyond. Trends Pharmacol Sci 2019; 40:267-277. [PMID: 30853109 PMCID: PMC6445269 DOI: 10.1016/j.tips.2019.02.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 12/18/2022]
Abstract
The endocannabinoid (eCB) signaling system modulates neurotransmission and inflammation, among other physiological functions. Its newest member, α/β-hydrolase domain-containing 6 (ABHD6), has emerged as a promising therapeutic target to treat several devastating diseases, including epilepsy. Here, we review the molecular mechanisms that mediate and control eCB signaling and, within it, the specific role of ABHD6. We also discuss how ABHD6 controls the abundance of additional lipids and the trafficking of ionotropic receptors to plasma membranes. We finish with several unexplored questions regarding this novel enzyme. Our current understanding of the molecular mechanism and biological function of ABHD6 provides a strong foundation for the development of small-molecule therapeutics to treat devastating diseases.
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Affiliation(s)
- Jessica K Cao
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Joshua Kaplan
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Nephi Stella
- Department of Pharmacology, University of Washington, Seattle, WA, USA; Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA.
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18
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Identification of novel PPARα/γ dual agonists by pharmacophore screening, docking analysis, ADMET prediction and molecular dynamics simulations. Comput Biol Chem 2019; 78:178-189. [DOI: 10.1016/j.compbiolchem.2018.11.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/20/2018] [Accepted: 11/25/2018] [Indexed: 01/05/2023]
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19
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Kind L, Kursula P. Structural properties and role of the endocannabinoid lipases ABHD6 and ABHD12 in lipid signalling and disease. Amino Acids 2018; 51:151-174. [PMID: 30564946 DOI: 10.1007/s00726-018-2682-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/23/2018] [Indexed: 12/18/2022]
Abstract
The endocannabinoid (eCB) system is an important part of both the human central nervous system (CNS) and peripheral tissues. It is involved in the regulation of various physiological and neuronal processes and has been associated with various diseases. The eCB system is a complex network composed of receptor molecules, their cannabinoid ligands, and enzymes regulating the synthesis, release, uptake, and degradation of the signalling molecules. Although the eCB system and the molecular processes of eCB signalling have been studied extensively over the past decades, the involved molecules and underlying signalling mechanisms have not been described in full detail. An example pose the two poorly characterised eCB-degrading enzymes α/β-hydrolase domain protein six (ABHD6) and ABHD12, which have been shown to hydrolyse 2-arachidonoyl glycerol-the main eCB in the CNS. We review the current knowledge about the eCB system and the role of ABHD6 and ABHD12 within this important signalling system and associated diseases. Homology modelling and multiple sequence alignments highlight the structural features of the studied enzymes and their similarities, as well as the structural basis of disease-related ABHD12 mutations. However, homologies within the ABHD family are very low, and even the closest homologues have widely varying substrate preferences. Detailed experimental analyses at the molecular level will be necessary to understand these important enzymes in full detail.
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Affiliation(s)
- Laura Kind
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway. .,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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20
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Liu X, Li W, Hu B, Wang M, Wang J, Guan L. Identification of isobavachalcone as a potential drug for rice blast disease caused by the fungus Magnaporthe grisea. J Biomol Struct Dyn 2018; 37:3399-3409. [PMID: 30132740 DOI: 10.1080/07391102.2018.1515117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The rice blast disease caused by the fungus Magnaporthe grisea is one of the most devastating rice diseases, but there is no effective fungicide toward chitinase which is a key enzyme of M. grisea. In this study, we observed that distortion and cell-wall damage of M. grisea hyphae were significantly under the scanning electron micrograph after a 24-h treatment with 10 mg/L isobavachalcone (IBC) extracted from Psoralea corylifolia L. To further explore the effect of IBC on the cell wall of M. grisea, we examined changes in enzymes associated with cell wall degradation by enzyme activity experiments, treated liquid culture mycelia with 10 mg/L IBC for 1 h. Results displayed that chitinase was obviously more active than control group. To illustrate the interactions between IBC and chitinase, the studies of homology modeling and molecular docking were carried out successively. The results revealed that IBC had hydrogen bonds with residues ASP267 and ARG276 of chitinase. Besides, these nonpolar residues TYR270, PRO271, VAL272, LEU310, PRO311, TYR316, and LEU317 were able to form strong hydrophobic interactions. Binding energies of the chitinase-IBC complexes were calculated by MM-GBSA showed that the ΔGbind score of molecular dynamics had lower binding energy and more stable than docking complexes. All above, IBC owns significant agonistic activity in chitinase and would be a potent fungicide to inhibit the growth of M. grisea. We hope the above information provides an important insight for understanding the interactions between IBC and chitinase, which may be useful in the discovery of a novel potent agonist. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xue Liu
- a Department of Pharmaceutical and Biological Engineering , Shenyang University of Chemical Technology , Shenyang , China
| | - Wei Li
- a Department of Pharmaceutical and Biological Engineering , Shenyang University of Chemical Technology , Shenyang , China
| | - Baichun Hu
- b Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education , Shenyang Pharmaceutical University , Shenyang , China
| | - Mingxing Wang
- b Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education , Shenyang Pharmaceutical University , Shenyang , China
| | - Jian Wang
- b Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education , Shenyang Pharmaceutical University , Shenyang , China
| | - Lijie Guan
- a Department of Pharmaceutical and Biological Engineering , Shenyang University of Chemical Technology , Shenyang , China
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21
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Wang M, Wang Y, Kong D, Jiang H, Wang J, Cheng M. In silico exploration of aryl sulfonamide analogs as voltage-gated sodium channel 1.7 inhibitors by using 3D-QSAR, molecular docking study, and molecular dynamics simulations. Comput Biol Chem 2018; 77:214-225. [PMID: 30359866 DOI: 10.1016/j.compbiolchem.2018.10.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/07/2018] [Accepted: 10/10/2018] [Indexed: 12/25/2022]
Abstract
It has been demonstrated by human genetics that the voltage-gated sodium channel Nav1.7 is currently a promising target for the treatment of pain. In this research, we performed molecular simulation works on a series of classic aryl sulfonamide Nav1.7 inhibitors using three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking and molecular dynamics (MD) simulations for the first time to explore the correlation between their structures and activities. The results of the relevant statistical parameters of comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analyses (CoMSIA) had been verified to be reasonable, and the deep relationship between the structures and activities of these inhibitors was obtained by analyzing the contour maps. The generated 3D-QSAR model showed a good predictive ability and provided valuable clues for the rational modification of molecules. The interactions between compounds and proteins were modeled by molecular docking studies. Finally, accuracy of the docking results and stability of the complexes were verified by 100 ns MD simulations. Detailed information on the key residues at the binding site and the types of interactions they participate in involved was obtained. The van der Waals energy contributed the most in the molecular binding process according to the calculation of binding free energy. All research results provided a good basis for further research on novel and effective Nav1.7 inhibitors.
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Affiliation(s)
- Mingxing Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China
| | - Ying Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China
| | - Dejiang Kong
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China
| | - Hailun Jiang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China.
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, China.
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22
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Swatko-Ossor M, Klimek K, Belcarz A, Kaczor AA, Pitucha M, Ginalska G. Do new N-substituted 3-amino-4-phenyl-5-oxo-pyrazolinecarboxamide derivatives exhibit antitubercular potential? Eur J Pharm Sci 2018; 121:155-165. [PMID: 29802898 DOI: 10.1016/j.ejps.2018.05.024] [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: 12/07/2017] [Revised: 04/20/2018] [Accepted: 05/23/2018] [Indexed: 11/27/2022]
Abstract
As a continuation of previous tests concerning new N-substituted 3-amino-4-phenyl-5-oxo-pyrazolinecarboxamide derivatives (R3, R4 and R8) of notable antibacterial activity, their antitubercular potential against different mycobacterial strains was estimated. Tests performed on virulent (reference and clinical) strains of Mycobacterium bovis and Mycobacterium tuberculosis revealed the highest therapeutic potential of R8 derivative: MIC within the range 7.8-15.6 μg/ml and TI (therapeutic index) within the range 46.5-93. Moreover, the synergistic interaction was found between R3, R4 and R8 derivatives and rifampicin, one of the front-line antitubercular drugs. R8/rifampicin mixture in concentrations effective in inhibition of Mycobacterium tuberculosis strain was non-cytotoxic against GMK cells, displaying cell viability approximately 88-97% when compared to control. Molecular docking study enabled to conclude that enoyl acyl carrier protein reductase (InhA) can be considered as a potential molecular target of tested pyrazole derivatives. Although further modifications of chemical structure of the investigated pyrazole derivatives is required, in order to increase their antitubercular efficacy and therapeutic safety, these compounds, in particular R8 compound, can be promising for the treatment of human and bovine tuberculosis.
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Affiliation(s)
- Marta Swatko-Ossor
- Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland
| | - Katarzyna Klimek
- Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland
| | - Anna Belcarz
- Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland.
| | - Agnieszka Anna Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Chodźki 4A, 20-093 Lublin, Poland; University of Eastern Finland, School of Pharmacy, Department of Pharmaceutical Chemistry, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Monika Pitucha
- Independent Radiopharmacy Unit Department of Organic Chemistry, Medical University of Lublin, Chodzki 4A, 20-093 Lublin, Poland
| | - Grazyna Ginalska
- Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland
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23
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Li W, Liu X, Muhammad S, Shi J, Meng Y, Wang J. Computational investigation of TGF-β receptor inhibitors for treatment of idiopathic pulmonary fibrosis: Field-based QSAR model and molecular dynamics simulation. Comput Biol Chem 2018; 76:139-150. [PMID: 30015175 DOI: 10.1016/j.compbiolchem.2018.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 10/28/2022]
Abstract
The discovery of drugs relevant to transforming growth factor β (TGF-β) receptor inhibitors have been considered as a considerable challenge during therapy idiopathic pulmonary fibrosis diseases. For the first time, herein we illustrate a field-based quantitative structure-activity relationship (QSAR) model and molecular dynamics (MD) simulations for novel 7-substituted-pyrazolo [4, 3-b] pyridine derivatives with biological activity for the TGF-β receptor, with an attempt of elucidating the 3D structural features that are essential for the activity. Results demonstrate that the field-based model (Q2 = 0.548, R2training = 0.840, R2test = 0.750) are acceptable with good predictive capabilities. In addition, MD studies were also carried out on the training set with the aim of exploring their binding modes in the active pocket of TGF-β receptor, resulting in some of the crucial structural fragments which are responsible for inhibitory activity. Therefore, we summarized the following features required for TGF-β receptor inhibition: electronegative in region1, bulky groups in region2 and smaller groups in region3. Based on the model and related information, we hope the above information provides an important insight for understanding the interactions of the inhibitors and TGF-β receptor, which may be useful in discovering novel potent inhibitors.
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Affiliation(s)
- Wei Li
- Department of Pharmaceutical Engineering, Shenyang University of Chemical Technology, Shenyang, China
| | - Xue Liu
- Department of Pharmaceutical Engineering, Shenyang University of Chemical Technology, Shenyang, China
| | - Suleiman Muhammad
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - JiYue Shi
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - YanQiu Meng
- Department of Pharmaceutical Engineering, Shenyang University of Chemical Technology, Shenyang, China.
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
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Molecular docking, 3D-QSAR and structural optimization on imidazo-pyridine derivatives dually targeting AT1 and PPARg. Oncotarget 2018; 8:25612-25627. [PMID: 28445965 PMCID: PMC5421955 DOI: 10.18632/oncotarget.15778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/27/2017] [Indexed: 12/14/2022] Open
Abstract
Telmisartan, a bifunctional agent of blood pressure lowering and glycemia reduction, was previously reported to antagonize angiotensin II type 1 (AT1) receptor and partially activate peroxisome proliferator-activated receptor γ (PPARγ) simultaneously. Through the modification to telmisartan, researchers designed and obtained imidazo-\pyridine derivatives with the IC50s of 0.49∼94.1 nM against AT1 and EC50s of 20∼3640 nM towards PPARγ partial activation. For minutely inquiring the interaction modes with the relevant receptor and analyzing the structure-activity relationships, molecular docking and 3D-QSAR (Quantitative structure-activity relationships) analysis of these imidazo-\pyridines on dual targets were conducted in this work. Docking approaches of these derivatives with both receptors provided explicit interaction behaviors and excellent matching degree with the binding pockets. The best CoMFA (Comparative Molecular Field Analysis) models exhibited predictive results of q2=0.553, r2=0.954, SEE=0.127, r2pred=0.779 for AT1 and q2=0.503, r2=1.00, SEE=0.019, r2pred=0.604 for PPARγ, respectively. The contour maps from the optimal model showed detailed information of structural features (steric and electrostatic fields) towards the biological activity. Combining the bioisosterism with the valuable information from above studies, we designed six molecules with better predicted activities towards AT1 and PPARγ partial activation. Overall, these results could be useful for designing potential dual AT1 antagonists and partial PPARγ agonists.
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Kaczor AA, Żuk J, Matosiuk D. Comparative molecular field analysis and molecular dynamics studies of the dopamine D 2 receptor antagonists without a protonatable nitrogen atom. Med Chem Res 2018; 27:1149-1166. [PMID: 29576721 PMCID: PMC5854747 DOI: 10.1007/s00044-018-2137-5] [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: 09/29/2015] [Accepted: 01/20/2018] [Indexed: 11/24/2022]
Abstract
The dopaminergic hypothesis of schizophrenia is the main concept explaining the direct reasons of schizophrenia and the effectiveness of current antipsychotics. All antipsychotics present on the market are potent dopamine D2 receptor antagonists or partial agonists. In this work we investigate a series of dopamine D2 receptor antagonists which do not fulfill the criteria of the classical pharmacophore model as they do not possess a protonatable nitrogen atom necessary to interact with the conserved Asp(3.32). Such compounds are interesting, inter alia, due to possible better pharmacokinetic profile when compared to basic, ionizable molecules. By means of homology modeling, molecular docking and molecular dynamics we determined that the compounds investigated interact with Asp(3.32) via their amide nitrogen atom. It was found that the studied compounds stabilize the receptor inactive conformation through the effect on the ionic lock, which is typical for GPCR antagonists. We constructed a CoMFA model for the studied compounds with the following statistics: R2 = 0.95, Q2 = 0.63. The quality of the CoMFA model was confirmed by high value of R2 of the test set, equal 0.96. The CoMFA model indicated two regions where bulky substituents are favored and two regions where bulky substituents are not beneficial. Two red contour regions near carbonyl groups were identified meaning that negative charge would be favored here. Furthermore, the S-oxide group is connected with blue contour region meaning that positive charge is favored in this position. These findings may be applied for further optimization of the studied compound series. ![]()
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Affiliation(s)
- Agnieszka A Kaczor
- 1Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Faculty of Pharmacy with Division of Medical Analytics, Medical University of Lublin, 4A Chodźki St., 20093 Lublin, Poland.,2School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, 70211 Kuopio, Finland
| | - Justyna Żuk
- 1Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Faculty of Pharmacy with Division of Medical Analytics, Medical University of Lublin, 4A Chodźki St., 20093 Lublin, Poland
| | - Dariusz Matosiuk
- 1Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Faculty of Pharmacy with Division of Medical Analytics, Medical University of Lublin, 4A Chodźki St., 20093 Lublin, Poland
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26
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On the virtues of automated quantitative structure-activity relationship: the new kid on the block. Future Med Chem 2018; 10:335-342. [PMID: 29393678 DOI: 10.4155/fmc-2017-0170] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Quantitative structure-activity relationship (QSAR) has proved to be an invaluable tool in medicinal chemistry. Data availability at unprecedented levels through various databases have collaborated to a resurgence in the interest for QSAR. In this context, rapid generation of quality predictive models is highly desirable for hit identification and lead optimization. We showcase the application of an automated QSAR approach, which randomly selects multiple training/test sets and utilizes machine-learning algorithms to generate predictive models. Results demonstrate that AutoQSAR produces models of improved or similar quality to those generated by practitioners in the field but in just a fraction of the time. Despite the potential of the concept to the benefit of the community, the AutoQSAR opportunity has been largely undervalued.
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Jia WQ, Jing Z, Liu X, Feng XY, Liu YY, Wang SQ, Xu WR, Liu JW, Cheng XC. Virtual identification of novel PPARα/γ dual agonists by scaffold hopping of saroglitazar. J Biomol Struct Dyn 2017; 36:3496-3512. [DOI: 10.1080/07391102.2017.1392363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wen-Qing Jia
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Zhi Jing
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xin Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Shu-Qing Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Jian-Wen Liu
- State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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28
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Design, sythesis and evaluation of a series of 3- or 4-alkoxy substituted phenoxy derivatives as PPARs agonists. Oncotarget 2017; 8:20766-20783. [PMID: 28186999 PMCID: PMC5400543 DOI: 10.18632/oncotarget.15198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 01/25/2017] [Indexed: 11/25/2022] Open
Abstract
Peroxisome proliferators-activated receptors (PPARα, γ and δ) are potentially effective targets for Type 2 diabetes mellitus therapy. The severe effects of known glitazones and the successfully approved agents (saroglitazar and lobeglitazone) motivated us to study novelly potent PPARs drugs with improved safety profile. In this work, we received 15 carboxylic acids based on the combination principle to integrate the polar head of bezafibrate with the hydrophobic tail of pioglitazone. Another 12 tetrazoles based on the bioisosterism principle were obtained accordingly. Furthermore, in vitro PPARs transactivation assays on these 3- or 4-alkoxy substituted phenoxy derivatives afforded six compounds. Interactions and binding stability from the docking analysis and 20 ns molecular dynamic simulations confirmed the representative compounds to be suitable and plausible for PPARs pockets. The above-mentioned results demonstrated that the compounds may be used as reference for further optimization for enhanced PPARs activities and wide safety range.
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29
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Zhang J, Liu X, Wang SQ, Liu GY, Xu WR, Cheng XC, Wang RL. Identification of dual ligands targeting angiotensin II type 1 receptor and peroxisome proliferator-activated receptor-γ by core hopping of telmisartan. J Biomol Struct Dyn 2016; 35:2665-2680. [PMID: 27602589 DOI: 10.1080/07391102.2016.1227726] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
It has been reported previously that some angiotensin II receptor blockers not only antagonize angiotensin II type 1 receptor (AT1R), but also exert stimulation in peroxisome proliferator-activated receptor γ (PPARγ) partial activation, among which telmisartan displays the best. Telmisartan has been tested as a bifunctional ligand with antihypertensive and hypoglycemic activity. Aiming at more potent leads with selective AT1R antagonism and PPARγ partial agonism, the three parts of telmisartan including the distal benzimidazole ring, the biphenyl moiety, and the carboxylic acid group experienced modification by core hopping method in our study. The central benzimidazole ring, however, remained intact considering its great affinity toward AT1R and PPARγ. We utilized computational techniques for the sake of details on the binding interactions and conformational stability. Standard precision docking analysis and absorption, distribution, metabolism, excretion, and toxicity prediction received 10 molecules with higher Glide scores, similar interactions, and improved pharmacokinetic profiles compared to telmisartan. Comp#91 with highest scores for AT1R (-11.92 kcal/mol) and PPARγ (-13.88 kcal/mol) exhibited excellent binding modes and pharmacokinetic parameters. Molecular dynamics trajectories on best docking pose of comp#91 confirmed the docking results and verified the conformational stability with both receptors throughout the course of 20-ns simulations. Thus, comp#91 could be identified as a promising lead in the development of dual AT1R antagonist and PPARγ partial agonist against hypertension and type 2 diabetes.
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Affiliation(s)
- Jun Zhang
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Xin Liu
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Shu-Qing Wang
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Gui-You Liu
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Wei-Ren Xu
- b Tianjin Key Laboratory of Molecular Design and Drug Discovery , Tianjin Institute of Pharmaceutical Research , Tianjin 300193 , China
| | - Xian-Chao Cheng
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Run-Ling Wang
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
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Patent Highlight. Pharm Pat Anal 2016. [DOI: 10.4155/ppa.15.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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