1
|
Selvan G T, Ashok AK, Rao S J A, Gollapalli P, R V, N SK, Chaudhury NK. Nrf2-regulated antioxidant response ameliorating ionizing radiation-induced damages explored through in vitro and molecular dynamics simulations. J Biomol Struct Dyn 2023; 41:8472-8484. [PMID: 36307909 DOI: 10.1080/07391102.2022.2137245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/06/2022] [Indexed: 10/31/2022]
Abstract
This study aims to investigate the mechanism of natural antioxidant ferulic acid (FA) in reducing oxidative stress followed by its inhibitory effect on the Keap1-Nrf2 complex. FA was treated ex vivo with human blood for 30 min at 37 °C ± 1 °C and exposed to 1.5 Gy of γ- rays of 60Co (0.789 Gy/min) and allowed for repair for an hour at 37 °C ± 1 °C. FA's free radical scavenging capacity was measured using 2,7-dichlorofluorescein diacetate assay and cytogenetic assays. Further, a possible mechanism of protein-ligand interaction between FA and Keap1-Nrf2 pathway protein as a cellular drug target was studied using docking and molecular dynamics simulation. The 1.5 Gy of γ- rays exposed to pre-treated blood with FA showed a significant (p < 0.05) reduction in reactive oxygen species and DNA damage compared to the normal control blood group sample. The ligand-protein transient binding interaction in molecular dynamic simulation over a period of 100 ns was consistent and stable emphasizing complementary charge between the protein and ligand, speculating higher hydrophobic amino acid residues in the Keap1 active pocket. This might sway the Keap1 from interaction with Nrf2, and could lead to nuclear translocation of Nrf2 during radiation-induced oxidative stress. The present study emphasizes the radioprotective effect of FA against 1.5 Gy of γ- rays exposed to human blood and the application of in silico approaches helpful for the possible protective effect of FA.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Tamizh Selvan G
- Central Research Laboratory, KS Hegde Medical Academy, Nitte (Deemed to be University), Mangalore, Karnataka, India
| | - Avinash Karkada Ashok
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, India
| | - Aditya Rao S J
- Kimberelite Chemicals India Pvt. Ltd, KIADB III Phase, Bangalore, Karnataka, India
| | - Pavan Gollapalli
- Center for Bioinformatics and Biostatistics, Nitte (Deemed to be University), Mangalore, Karnataka, India
| | - Vishakh R
- Central Research Laboratory, KS Hegde Medical Academy, Nitte (Deemed to be University), Mangalore, Karnataka, India
| | - Suchetha Kumari N
- Central Research Laboratory, KS Hegde Medical Academy, Nitte (Deemed to be University), Mangalore, Karnataka, India
| | - Nabo K Chaudhury
- Division of Radiation Biodosimetry, Institute of Nuclear Medicine and Allied Sciences-Defence Research and Development Organisation (DRDO), Delhi, India
| |
Collapse
|
2
|
Yang CS, Wu MC, Lai MC, Wu SN, Huang CW. Identification of New Antiseizure Medication Candidates in Preclinical Animal Studies. Int J Mol Sci 2023; 24:13143. [PMID: 37685950 PMCID: PMC10487685 DOI: 10.3390/ijms241713143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/09/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Epilepsy is a multifactorial neurologic disease that often leads to many devastating disabilities and an enormous burden on the healthcare system. Until now, drug-resistant epilepsy has presented a major challenge for approximately 30% of the epileptic population. The present article summarizes the validated rodent models of seizures employed in pharmacological researches and comprehensively reviews updated advances of novel antiseizure candidates in the preclinical phase. Newly discovered compounds that demonstrate antiseizure efficacy in preclinical trials will be discussed in the review. It is inspiring that several candidates exert promising antiseizure activities in drug-resistant seizure models. The representative compounds consist of derivatives of hybrid compounds that integrate multiple approved antiseizure medications, novel positive allosteric modulators targeting subtype-selective γ-Aminobutyric acid type A receptors, and a derivative of cinnamamide. Although the precise molecular mechanism, pharmacokinetic properties, and safety are not yet fully clear in every novel antiseizure candidate, the adapted approaches to design novel antiseizure medications provide new insights to overcome drug-resistant epilepsy.
Collapse
Affiliation(s)
- Chih-Sheng Yang
- Department of Neurology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung City 42743, Taiwan;
- School of Post-Baccalaureate Chinese Medicine, Tzu Chi University, Hualien City 97004, Taiwan
| | - Man-Chun Wu
- Department of Family Medicine and Preventive Medicine Center, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung City 42743, Taiwan
| | - Ming-Chi Lai
- Department of Pediatrics, Chi-Mei Medical Center, Tainan City 71004, Taiwan;
| | - Sheng-Nan Wu
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan City 70101, Taiwan;
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan City 70101, Taiwan
| | - Chin-Wei Huang
- Department of Neurology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City 70101, Taiwan
| |
Collapse
|
3
|
Pan T, He M, Deng L, Li J, Fan Y, Hao X, Mu S. Design, Synthesis, and Evaluation of the COX-2 Inhibitory Activities of New 1,3-Dihydro- 2H-indolin-2-one Derivatives. Molecules 2023; 28:4668. [PMID: 37375225 DOI: 10.3390/molecules28124668] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Thirty-three 1,3-dihydro-2H-indolin-2-one derivatives bearing α, β-unsaturated ketones were designed and synthesized via the Knoevenagel condensation reaction. The cytotoxicity, in vitro anti-inflammatory ability, and in vitro COX-2 inhibitory activity of all the compounds were evaluated. Compounds 4a, 4e, 4i-4j, and 9d exhibited weak cytotoxicity and different degrees of inhibition against NO production in LPS-stimulated RAW 264.7 cells. The IC50 values of compounds 4a, 4i, and 4j were 17.81 ± 1.86 μM, 20.41 ± 1.61 μM, and 16.31 ± 0.35 μM, respectively. Compounds 4e and 9d showed better anti-inflammatory activity with IC50 values of 13.51 ± 0.48 μM and 10.03 ± 0.27 μM, respectively, which were lower than those of the positive control ammonium pyrrolidinedithiocarbamate (PDTC). Compounds 4e, 9h, and 9i showed good COX-2 inhibitory activities with IC50 values of 2.35 ± 0.04 µM, 2.422 ± 0.10 µM and 3.34 ± 0.05 µM, respectively. Moreover, the possible mechanism by which COX-2 recognized 4e, 9h, and 9i was predicted by molecular docking. The results of this research suggested that compounds 4e, 9h, and 9i might be new anti-inflammatory lead compounds for further optimization and evaluation.
Collapse
Affiliation(s)
- Taohua Pan
- College of Pharmacy, Guizhou University, Guiyang 550025, China
| | - Maofei He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academy of Sciences, Guiyang 550014, China
| | - Lulu Deng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academy of Sciences, Guiyang 550014, China
| | - Jiang Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academy of Sciences, Guiyang 550014, China
| | - Yanhua Fan
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academy of Sciences, Guiyang 550014, China
| | - Xiaojiang Hao
- Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming 650201, China
| | - Shuzhen Mu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academy of Sciences, Guiyang 550014, China
| |
Collapse
|
4
|
Xin M, Wu H, Du Y, Liu S, Zhao F, Mou X. Synthesis and biological evaluation of resveratrol amide derivatives as selective COX-2 inhibitors. Chem Biol Interact 2023; 380:110522. [PMID: 37179037 DOI: 10.1016/j.cbi.2023.110522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/15/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
Selective COX-2 inhibitors have been considered to be reliable alternatives to tNSAIDs, but most of them were withdrawn from the market due to their risk of heart attack and stroke. Therefore, it is urgent to develop a new type of selective COX-2 inhibitor with high efficiency and low toxicity. Inspired by the cardiovascular protection, and anti-inflammatory activity of resveratrol, we synthesized 38 resveratrol amide derivatives and evaluated their COX-1/COX-2 inhibitory activities. Compounds 8a, 6a, 8c and 13c showed important inhibitory activity against COX-2 (IC50 = 0.42-2.54 μM) with definite selectivity (SI = 48-83). Molecular docking study demonstrated that these compounds partially entered the 2°-pocket of the COX-2 active site and interacted with the amino acid residues responsible for the COX-2 selectivity, which was in a similar orientation and binding interactions to rofecoxib. Further anti-inflammatory activity evaluation in vivo of these active compounds revealed that compound 8a showed no gastric ulcer toxicity, and displayed evident anti-inflammatory effect (45.95% inhibition of edema) with three oral doses of 50 mg/kg, which is worthy of further study. Moreover, compounds 6a and 8c also exhibited superior gastric safety profiles compared to the reference drugs celecoxib and indomethacin.
Collapse
Affiliation(s)
- Min Xin
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, Yantai, 264005, PR China
| | - Haoyu Wu
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, Yantai, 264005, PR China
| | - Yuan Du
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, Yantai, 264005, PR China
| | - Sheng Liu
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, Yantai, 264005, PR China
| | - Feng Zhao
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, Yantai, 264005, PR China
| | - Xiaofeng Mou
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Yantai University, Yantai, 264005, PR China.
| |
Collapse
|
5
|
Nandi R, Bhowmik D, Srivastava R, Prakash A, Kumar D. Discovering potential inhibitors against SARS-CoV-2 by targeting Nsp13 Helicase. J Biomol Struct Dyn 2022; 40:12062-12074. [PMID: 34455933 DOI: 10.1080/07391102.2021.1970024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The rise in the incidence of COVID-19 as a result of SARS-CoV-2 infection has threatened public health globally. Till now, there have been no proper prophylactics available to fight COVID-19, necessitating the advancement and evolution of effective curative against SARS-CoV-2. This study aimed at the nonstructural protein 13 (nsp13) helicase as a promising target for drug development against COVID-19. A unique collection of nucleoside analogs was screened against the SARS-CoV-2 helicase protein, for which a molecular docking experiment was executed to depict the selected ligand's binding affinity with the SARS-CoV-2 helicase proteins. Simultaneously, molecular dynamic simulations were performed to examine the protein's binding site's conformational stability, flexibility, and interaction with the ligands. Key nucleoside ligands were selected for pharmacokinetic analysis based on their docking scores. Selected ligands (cordycepin and pritelivir) showed excellent pharmacokinetics and were well stabilized at the proteins' binding site throughout the MD simulation. We have also performed binding free energy analysis or the binding characteristics of ligands with Nsp13 by using MM-PBSA and MM-GBSA. Free energy calculation by MM-PBSA and MM-GBSA analysis suggests that pritelivir may work as viable therapeutics for efficient drug advancement against SARS-CoV-2 Nsp13 helicase, potentially arresting the SARS-CoV-2 replication.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Rajat Nandi
- Department of Microbiology, Assam University, Silchar, Assam, India
| | - Deep Bhowmik
- Department of Microbiology, Assam University, Silchar, Assam, India
| | - Rakesh Srivastava
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, Haryana, India
| | - Diwakar Kumar
- Department of Microbiology, Assam University, Silchar, Assam, India
| |
Collapse
|
6
|
Yu J, Cheng Y, Cui Y, Zhai Y, Zhang W, Zhang M, Xin W, Liang J, Pan X, Wang Q, Sun H. Anti-Seizure and Neuronal Protective Effects of Irisin in Kainic Acid-Induced Chronic Epilepsy Model with Spontaneous Seizures. Neurosci Bull 2022; 38:1347-1364. [PMID: 35821335 PMCID: PMC9672298 DOI: 10.1007/s12264-022-00914-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
An increased level of reactive oxygen species is a key factor in neuronal apoptosis and epileptic seizures. Irisin reportedly attenuates the apoptosis and injury induced by oxidative stress. Therefore, we evaluated the effects of exogenous irisin in a kainic acid (KA)-induced chronic spontaneous epilepsy rat model. The results indicated that exogenous irisin significantly attenuated the KA-induced neuronal injury, learning and memory defects, and seizures. Irisin treatment also increased the levels of brain-derived neurotrophic factor (BDNF) and uncoupling protein 2 (UCP2), which were initially reduced following KA administration. Furthermore, the specific inhibitor of UCP2 (genipin) was administered to evaluate the possible protective mechanism of irisin. The reduced apoptosis, neurodegeneration, and spontaneous seizures in rats treated with irisin were significantly reversed by genipin administration. Our findings indicated that neuronal injury in KA-induced chronic epilepsy might be related to reduced levels of BDNF and UCP2. Moreover, our results confirmed the inhibition of neuronal injury and epileptic seizures by exogenous irisin. The protective effects of irisin may be mediated through the BDNF-mediated UCP2 level. Our results thus highlight irisin as a valuable therapeutic strategy against neuronal injury and epileptic seizures.
Collapse
Affiliation(s)
- Jie Yu
- School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Yao Cheng
- School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Yaru Cui
- School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Yujie Zhai
- School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Wenshen Zhang
- The Sixth Scientific Research Department, Shandong Institute of Nonmetallic Materials, Jinan, 250031, China
| | - Mengdi Zhang
- School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Wenyu Xin
- School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Jia Liang
- School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Xiaohong Pan
- School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, 264003, China
| | - Qiaoyun Wang
- School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, 264003, China.
| | - Hongliu Sun
- School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, 264003, China.
| |
Collapse
|
7
|
Jaiswal S, Gupta G, Ayyannan SR. Synthesis and evaluation of carbamate derivatives as fatty acid amide hydrolase and monoacylglycerol lipase inhibitors. Arch Pharm (Weinheim) 2022; 355:e2200081. [PMID: 35924298 DOI: 10.1002/ardp.202200081] [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: 02/14/2022] [Revised: 06/24/2022] [Accepted: 07/11/2022] [Indexed: 11/06/2022]
Abstract
Fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase (MAGL) are the primary catabolic enzymes for endocannabinoids, anandamide (AEA), and 2-arachidonoyl glycerol. Numerous studies have shown that FAAH and MAGL play an important role in modulating various central nervous system activities; hence, the development of small molecule FAAH/MAGL inhibitors is an active area of research. Several small molecules possessing the carbamate scaffold are documented as potential FAAH/MAGL inhibitors. Here, we designed and synthesized a series of open chain and cyclic carbamates and evaluated their dual FAAH-MAGL inhibition properties. Phenyl [4-(piperidin-1-ylmethyl)phenyl]carbamate (2e) emerged as the most potent MAGL inhibitor (IC50 = 19 nM), benzyl (1H-benzo[d]imidazol-2-yl)carbamate (3h) was the most potent FAAH inhibitor (IC50 = 55 nM), and phenyl (6-fluorobenzo[d]thiazol-2-yl)carbamate (2i) egressed as a nonselective dual FAAH-MAGL inhibitor (FAAH: 82 nM, MAGL: 72 nM). The enzyme kinetics experiments revealed that the compounds inhibit FAAH/MAGL in a covalent-reversible manner, with a mixed binding mode of action. Moreover, the lead compounds were found suitable for blood-brain permeation in the parallel artificial membrane permeation assay. Furthermore, docking simulation experiments suggested that the potency of the lead compounds was governed by hydrogen bonds and hydrophobic interactions with the enzyme active sites. In silico drug-likeness and ADMETox prediction studies provided useful information on the compounds' oral absorption, metabolism, and toxicity profiles. In summary, this study afforded potent multifunctional carbamates with appreciable pharmacokinetic profiles meriting further investigation.
Collapse
Affiliation(s)
- Shivani Jaiswal
- Pharmaceutical Chemistry Research Laboratory II, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, India
| | - Garima Gupta
- Pharmaceutical Chemistry Research Laboratory II, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, India
| | - Senthil R Ayyannan
- Pharmaceutical Chemistry Research Laboratory II, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, India
| |
Collapse
|
8
|
Oyewusi HA, Wu YS, Safi SZ, Wahab RA, Hatta MHM, Batumalaie K. Molecular dynamics simulations reveal the inhibitory mechanism of Withanolide A against α-glucosidase and α-amylase. J Biomol Struct Dyn 2022:1-16. [PMID: 35904027 DOI: 10.1080/07391102.2022.2104375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Diabetes mellitus (DM) is a global chronic disease characterized by hyperglycemia and insulin resistance. The unsavory severe gastrointestinal side-effects of synthetic drugs to regulate hyperglycemia have warranted the search for alternative treatments to inhibit the carbohydrate digestive enzymes (e.g. α-amylase and α-glucosidase). Certain phytochemicals recently captured the scientific community's attention as carbohydrate digestive enzyme inhibitors due to their low toxicity and high efficacy, specifically the Withanolides-loaded extract of Withania somnifera. That said, the present study evaluated in silico the efficacy of Withanolide A in targeting both α-amylase and α-glucosidase in comparison to the synthetic drug Acarbose. Protein-ligand interactions, binding affinity, and stability were characterized using pharmacological profiling, high-end molecular docking, and molecular-dynamic simulation. Withanolide A inhibited the activity of α-glucosidase and α-amylase better, exhibiting good pharmacokinetic properties, absorption, and metabolism. Also, Withanolide A was minimally toxic, with higher bioavailability. Interestingly, Withanolide A bonded well to the active site of α-amylase and α-glucosidase, yielding the lowest binding free energy of -82.144 ± 10.671 kcal/mol and -102.1043 ± 11.231 kcal/mol compared to the Acarbose-enzyme complexes (-63.220 ± 13.283 kcal/mol and -82.148 ± 10.671 kcal/mol). Hence, the findings supported the therapeutic potential of Withanolide A as α-amylase and α-glucosidase inhibitor for DM treatment.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Science Technology, Biochemistry unit, The Federal Polytechnic, Ado Ekiti, Ekiti State, Nigeria
| | - Yuan-Seng Wu
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Subang Jaya, Malaysia.,Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Sher Zaman Safi
- IRCBM, COMSATS University Islamabad, Lahore Campus, Punjab, Pakistan
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | | | - Kalaivani Batumalaie
- Department of Biomedical Science, Faculty of Health Sciences, Asia Metropolitan University, Johor Bahru, Johor, Malaysia
| |
Collapse
|
9
|
Prasanna P, Joshi T, Pant M, Pundir H, Chandra S. Evaluation of the inhibitory potential of Valproic acid against histone deacetylase of Leishmania donovani and computational studies of Valproic acid derivatives. J Biomol Struct Dyn 2022:1-18. [PMID: 35706132 DOI: 10.1080/07391102.2022.2087103] [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: 10/18/2022]
Abstract
Valproic acid (VA) is a proven inhibitor of human histone deacetylases (HDACs). The homogenous HDAC has been associated with all major human parasitic pathogens and hence, it has been considered an attractive drug target for anti-leishmanial therapy. To assist in drug design endeavors for HDACs, an in-vitro study has been presented to investigate the VA inhibition on Leishmania donovani HDAC (LdHDAC). The regression analysis of VA by 24 hrs viability assay confirmed its activity against LdHDAC. Moreover, the toxicity of VA is also well documented. Thus, the in-silico experiments were also conducted to screen the non-toxic VA derivatives as anti-leishmanial drug candidates having potential as inhibitors of LdHDAC. For in-silico study, the 3D structure of target LdHDAC was developed by homology modeling. Based on their in-silico activity, we shortlisted 13 VA derivatives having maximum affinity for LdHDAC and identified four potential derivatives that can specifically bind to this protein. After that, these ligands were subjected to molecular dynamics simulation. These derivatives may be effective against L. donovani promastigotes since they followed Lipinski's RO5 and were non-toxic. Thus, screened derivatives can be considered as lead ligands for targeting LdHDAC and may be used as possible drug candidates to treat leishmaniasis and overcome the limitation of anti-leishmanial drugs. This is the first report of antileishmanial potential of VA and its derivatives targeting LdHDAC. Hence, the current investigation presents a search for novel target specific drugs to aid the anti-leishmanial drug development. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Pragya Prasanna
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Vaishali, India
| | - Tanuja Joshi
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Manish Pant
- Department of Post-Harvest Process and Food Engineering, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Hemlata Pundir
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| |
Collapse
|
10
|
Kumar N, Srivastava R, Mongre RK, Mishra CB, Kumar A, Khatoon R, Banerjee A, Ashraf-Uz-Zaman M, Singh H, Lynn AM, Lee MS, Prakash A. Identifying the Novel Inhibitors Against the Mycolic Acid Biosynthesis Pathway Target "mtFabH" of Mycobacterium tuberculosis. Front Microbiol 2022; 13:818714. [PMID: 35602011 PMCID: PMC9121832 DOI: 10.3389/fmicb.2022.818714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/28/2022] [Indexed: 11/18/2022] Open
Abstract
Mycolic acids are the key constituents of mycobacterial cell wall, which protect the bacteria from antibiotic susceptibility, helping to subvert and escape from the host immune system. Thus, the enzymes involved in regulating and biosynthesis of mycolic acids can be explored as potential drug targets to kill Mycobacterium tuberculosis (Mtb). Herein, Kyoto Encyclopedia of Genes and Genomes is used to understand the fatty acid metabolism signaling pathway and integrative computational approach to identify the novel lead molecules against the mtFabH (β-ketoacyl-acyl carrier protein synthase III), the key regulatory enzyme of the mycolic acid pathway. The structure-based virtual screening of antimycobacterial compounds from ChEMBL library against mtFabH results in the selection of 10 lead molecules. Molecular binding and drug-likeness properties of lead molecules compared with mtFabH inhibitor suggest that only two compounds, ChEMBL414848 (C1) and ChEMBL363794 (C2), may be explored as potential lead molecules. However, the spatial stability and binding free energy estimation of thiolactomycin (TLM) and compounds C1 and C2 with mtFabH using molecular dynamics simulation, followed by molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) indicate the better activity of C2 (ΔG = -14.18 kcal/mol) as compared with TLM (ΔG = -9.21 kcal/mol) and C1 (ΔG = -13.50 kcal/mol). Thus, compound C1 may be explored as promising drug candidate for the structure-based drug designing of mtFabH inhibitors in the therapy of Mtb.
Collapse
Affiliation(s)
- Niranjan Kumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Srivastava
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Raj Kumar Mongre
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women’s University, Seoul, South Korea
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Chandra Bhushan Mishra
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, United States
| | - Amit Kumar
- Indian Council of Medical Research–Computational Genomics Centre, All India Institute of Medical Research, New Delhi, India
- Amity Institute of Integrative Sciences and Health, Amity University, Gurugram, India
| | - Rosy Khatoon
- Amity Institute of Biotechnology, Amity University, Gurugram, India
| | - Atanu Banerjee
- Amity Institute of Biotechnology, Amity University, Gurugram, India
| | - Md Ashraf-Uz-Zaman
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, United States
| | - Harpreet Singh
- Indian Council of Medical Research–Computational Genomics Centre, All India Institute of Medical Research, New Delhi, India
| | - Andrew M. Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Myeong-Sok Lee
- Molecular Cancer Biology Laboratory, Cellular Heterogeneity Research Center, Department of Biosystem, Sookmyung Women’s University, Seoul, South Korea
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University, Gurugram, India
| |
Collapse
|
11
|
Jaiswal S, Akhilesh, Uniyal A, Tiwari V, Raja Ayyannan S. Synthesis and evaluation of dual fatty acid amide hydrolase-monoacylglycerol lipase inhibition and antinociceptive activities of 4-methylsulfonylaniline-derived semicarbazones. Bioorg Med Chem 2022; 60:116698. [PMID: 35296453 DOI: 10.1016/j.bmc.2022.116698] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/10/2022] [Accepted: 03/02/2022] [Indexed: 12/31/2022]
Abstract
Fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase (MAGL) are promising targets for neuropathic pain and other CNS disorders. Based on our previous lead compound SIH 3, we designed and synthesized a series of 4-methylsulfonylphenyl semicarbazones and evaluated for FAAH and MAGL inhibition properties. Most of the compounds showed potency towards both enzymes with leading FAAH selectivity. Compound (Z)-2-(2,6-dichlorobenzylidene)-N-(4-(methylsulfonyl)phenyl)hydrazine-1-carboxamide emerged as the lead inhibitor against both FAAH (IC50 = 11 nM) and MAGL (IC50 = 36 nM). The lead inhibitor inhibited FAAH by non-competitive mode, but showed a mixed-type inhibition against MAGL. Molecular docking study unveiled that the docked ligands bind favorably to the active sites of FAAH and MAGL. The lead inhibitor interacted with FAAH and MAGL via π-π stacking via phenyl ring and hydrogen bonding through sulfonyl oxygen atoms or amide NH. Moreover, the stability of docked complexes was rationalized by molecular simulation studies. PAMPA assay revealed that the lead compound is suitable for blood-brain penetration. The lead compound showed better cell viability in lipopolysaccharide-induced neurotoxicity assay in SH-SY5Y cell lines. Further, in-vivo experiments unveiled that dual inhibitor was safe up to 2000 mg/kg with no hepatotoxicity. The dual FAAH-MAGL inhibitor produced significant anti-nociceptive effect in the CCI model of neuropathic pain without altering locomotion activity. Lastly, the lead compound exhibited promising ex-vivo FAAH/MAGL inhibition activity at the dose of 10 mg/kg and 20 mg/kg. Thus, these findings suggest that the semicarbazone-based lead compound can be a potential template for the development of agents for neuropathic pain.
Collapse
Affiliation(s)
- Shivani Jaiswal
- Pharmaceutical Chemistry Research Laboratory II, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi - 221005, Uttar Pradesh, India
| | - Akhilesh
- Neuroscience and Pain Research Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Ankit Uniyal
- Neuroscience and Pain Research Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Vinod Tiwari
- Neuroscience and Pain Research Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Senthil Raja Ayyannan
- Pharmaceutical Chemistry Research Laboratory II, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi - 221005, Uttar Pradesh, India.
| |
Collapse
|
12
|
Amarnath Jonniya N, Sk MF, Kar P. Elucidating specificity of an allosteric inhibitor WNK476 among With‐No‐Lysine kinase isoforms using molecular dynamic simulations. Chem Biol Drug Des 2021; 98:405-420. [DOI: 10.1111/cbdd.13863] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/19/2021] [Accepted: 05/01/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering Indian Institute of Technology Indore Indore India
| | - Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering Indian Institute of Technology Indore Indore India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering Indian Institute of Technology Indore Indore India
| |
Collapse
|
13
|
Mishra CB, Kumari S, Angeli A, Bua S, Mongre RK, Tiwari M, Supuran CT. Discovery of Potent Carbonic Anhydrase Inhibitors as Effective Anticonvulsant Agents: Drug Design, Synthesis, and In Vitro and In Vivo Investigations. J Med Chem 2021; 64:3100-3114. [PMID: 33721499 DOI: 10.1021/acs.jmedchem.0c01889] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two sets of benzenesulfonamide-based effective human carbonic anhydrase (hCA) inhibitors have been developed using the tail approach. The inhibitory action of these novel molecules was examined against four isoforms: hCA I, hCA II, hCA VII, and hCA XII. Most of the molecules disclosed low to medium nanomolar range inhibition against all tested isoforms. Some of the synthesized derivatives selectively inhibited the epilepsy-involved isoforms hCA II and hCA VII, showing low nanomolar affinity. The anticonvulsant activity of selected sulfonamides was assessed using the maximal electroshock seizure (MES) and subcutaneous pentylenetetrazole (sc-PTZ) in vivo models of epilepsy. These potent CA inhibitors effectively inhibited seizures in both epilepsy models. The most effective compounds showed long duration of action and abolished MES-induced seizures up to 6 h after drug administration. These sulfonamides were found to be orally active anticonvulsants, being nontoxic in neuronal cell lines and in animal models.
Collapse
Affiliation(s)
- Chandra Bhushan Mishra
- College of Pharmacy, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul 04310, Republic of Korea
| | - Shikha Kumari
- Bio-Organic Chemistry Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Andrea Angeli
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Universitàdegli Studi di Firenze, Florence 50019, Italy
| | - Silvia Bua
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Universitàdegli Studi di Firenze, Florence 50019, Italy
| | - Raj Kumar Mongre
- College of Pharmacy, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul 04310, Republic of Korea
| | - Manisha Tiwari
- Bio-Organic Chemistry Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Universitàdegli Studi di Firenze, Florence 50019, Italy
| |
Collapse
|
14
|
Saha S, Nandi R, Vishwakarma P, Prakash A, Kumar D. Discovering Potential RNA Dependent RNA Polymerase Inhibitors as Prospective Drugs Against COVID-19: An in silico Approach. Front Pharmacol 2021; 12:634047. [PMID: 33716752 PMCID: PMC7952625 DOI: 10.3389/fphar.2021.634047] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/29/2021] [Indexed: 12/21/2022] Open
Abstract
COVID-19, caused by Severe Acute Respiratory Syndrome Corona Virus 2, is declared a Global Pandemic by WHO in early 2020. In the present situation, though more than 180 vaccine candidates with some already approved for emergency use, are currently in development against SARS-CoV-2, their safety and efficacy data is still in a very preliminary stage to recognize them as a new treatment, which demands an utmost emergency for the development of an alternative anti-COVID-19 drug sine qua non for a COVID-19 free world. Since RNA-dependent RNA polymerase (RdRp) is an essential protein involved in replicating the virus, it can be held as a potential drug target. We were keen to explore the plant-based product against RdRp and analyze its inhibitory potential to treat COVID-19. A unique collection of 248 plant compounds were selected based on their antiviral activity published in previous literature and were subjected to molecular docking analysis against the catalytic sub-unit of RdRp. The docking study was followed by a pharmacokinetics analysis and molecular dynamics simulation study of the selected best-docked compounds. Tellimagrandin I, SaikosaponinB2, Hesperidin and (-)-Epigallocatechin Gallate were the most prominent ones that showed strong binding affinity toward RdRp. All the compounds mentioned showed satisfactory pharmacokinetics properties and remained stabilized at their respective binding sites during the Molecular dynamics simulation. Additionally, we calculated the free-binding energy/the binding properties of RdRp-ligand complexes with the connection of MM/GBSA. Interestingly, we observe that SaikosaponinB2 gives the best binding affinity (∆Gbinding = -42.43 kcal/mol) in the MM/GBSA assay. Whereas, least activity is observed for Hesperidin (∆Gbinding = -22.72 kcal/mol). Overall our study unveiled the feasibility of the SaikosaponinB2 to serve as potential molecules for developing an effective therapy against COVID-19 by inhibiting one of its most crucial replication proteins, RdRp.
Collapse
Affiliation(s)
- Satabdi Saha
- Department of Microbiology, Assam University, Silchar, India
| | - Rajat Nandi
- Department of Microbiology, Assam University, Silchar, India
| | - Poonam Vishwakarma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, India
| | - Diwakar Kumar
- Department of Microbiology, Assam University, Silchar, India
| |
Collapse
|
15
|
Jha M, Alam O, Naim MJ, Sharma V, Bhatia P, Sheikh AA, Nawaz F, Alam P, Manaithiya A, Kumar V, Nazar S, Siddiqui N. Recent advancement in the discovery and development of anti-epileptic biomolecules: An insight into structure activity relationship and Docking. Eur J Pharm Sci 2020; 153:105494. [PMID: 32730845 DOI: 10.1016/j.ejps.2020.105494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/20/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022]
Abstract
Although there have been many advancements in scientific research and development, the cause of epilepsy still remains an open challenge. In spite of high throughput research in the field of anti-epileptic drugs, efficacy void is still prevalent before the researchers. Researchers have persistently been exploring all the possibilities to curb undesirable side effects of the anti-epileptic drugs or looking for a more substantial approach to diminish or cure epilepsy. The drug development has shown a hope to medicinal chemists and researchers to carry further research by going through a substantial literature survey. This review article attempts to describe the recent developments in the anti-epileptic agents, pertaining to different molecular scaffolds considering their structure-activity relationship, docking studies and their mechanism of actions.
Collapse
Affiliation(s)
- Mukund Jha
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Ozair Alam
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India.
| | - Mohd Javed Naim
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Vrinda Sharma
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Parth Bhatia
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Aadil Ahmad Sheikh
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Farah Nawaz
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Perwaiz Alam
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Ajay Manaithiya
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Vivek Kumar
- Department of Cardiology, Fortis Heart Institute, New Delhi, 110025, India
| | - Shagufi Nazar
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Nadeem Siddiqui
- Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| |
Collapse
|
16
|
Pandey P, Rane JS, Chatterjee A, Kumar A, Khan R, Prakash A, Ray S. Targeting SARS-CoV-2 spike protein of COVID-19 with naturally occurring phytochemicals: an in silico study for drug development. J Biomol Struct Dyn 2020; 39:6306-6316. [PMID: 32698689 PMCID: PMC7441770 DOI: 10.1080/07391102.2020.1796811] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Spike glycoprotein, a class I fusion protein harboring the surface of SARS-CoV-2
(SARS-CoV-2S), plays a seminal role in the viral infection starting from recognition of
the host cell surface receptor, attachment to the fusion of the viral envelope with the
host cells. Spike glycoprotein engages host Angiotensin-converting enzyme 2 (ACE2)
receptors for entry into host cells, where the receptor recognition and attachment of
spike glycoprotein to the ACE2 receptors is a prerequisite step and key determinant of the
host cell and tissue tropism. Binding of spike glycoprotein to the ACE2 receptor triggers
a cascade of structural transitions, including transition from a metastable pre-fusion to
a post-fusion form, thereby allowing membrane fusion and internalization of the virus.
From ancient times people have relied on naturally occurring substances like
phytochemicals to fight against diseases and infection. Among these phytochemicals,
flavonoids and non-flavonoids have been the active sources of different anti-microbial
agents. We performed molecular docking studies using 10 potential naturally occurring
compounds (flavonoids/non-flavonoids) against the SARS-CoV-2 spike protein and compared
their affinity with an FDA approved repurposed drug hydroxychloroquine (HCQ). Further, our
molecular dynamics (MD) simulation and energy landscape studies with fisetin, quercetin,
and kamferol revealed that these molecules bind with the hACE2-S complex with low binding
free energy. The study provided an indication that these molecules might have the
potential to perturb the binding of hACE2-S complex. In addition, ADME analysis also
suggested that these molecules consist of drug-likeness property, which may be further
explored as anti-SARS-CoV-2 agents. Communicated by Ramaswamy H. Sarma
Collapse
Affiliation(s)
- Preeti Pandey
- Department of Chemistry & Biochemistry, University of Oklahoma, OK, USA
| | - Jitendra Subhash Rane
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Aroni Chatterjee
- Indian Council of Medical Research (ICMR)-Virus Research Laboratory, NICED, Kolkata, India
| | - Abhijeet Kumar
- Department of Chemistry, Mahatma Gandhi Central University, Motihari, India
| | - Rajni Khan
- Motihari College of Engineering, Motihari, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, India
| | - Shashikant Ray
- Department of Biotechnology, Mahatma Gandhi Central University, Motihari, India
| |
Collapse
|
17
|
Rane JS, Pandey P, Chatterjee A, Khan R, Kumar A, Prakash A, Ray S. Targeting virus-host interaction by novel pyrimidine derivative: an in silico approach towards discovery of potential drug against COVID-19. J Biomol Struct Dyn 2020; 39:5768-5778. [PMID: 32684109 PMCID: PMC7441775 DOI: 10.1080/07391102.2020.1794969] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The entire human population over the globe is currently facing appalling conditions due
to the spread of infection from coronavirus disease-2019 (COVID-19). The spike
glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) present on
the surface of the virion mediates the virus entry into the host cells and therefore is
targeted by several scientific groups as a novel drug target site. The spike glycoprotein
binds to the human angiotensin-converting enzyme-2 (hACE2) cell surface receptor
abundantly expressed in lung tissues, and this binding phenomenon is a primary determinant
of cell tropism and pathogenesis. The binding and internalization of the virus is the
primary and most crucial step in the process of infection, and therefore the molecules
targeting the inhibition of this process certainly hold a significant therapeutic value.
Thus, we systematically applied the computational techniques to identify the plausible
inhibitor from a chosen set of well characterized diaryl pyrimidine analogues which may
disrupt interfacial interaction of spike glycoprotein (S) at the surface of hACE2. Using
molecular docking, molecular dynamics (MD) simulation and binding free energy calculation,
we have identified AP-NP (2-(2-amino-5-(naphthalen-2-yl)pyrimidin-4-yl)phenol),
AP-3-OMe-Ph (2-(2-amino-5-(3-methoxyphenyl)pyrimidin-4-yl)phenol) and AP-4-Me-Ph
(2-(2-amino-5-(p-tolyl) pyrimidin-4-yl)phenol) from a group of diaryl pyrimidine
derivatives which appears to bind at the interface of the hACE2-S complex with low binding
free energy. Thus, pyrimidine derivative AP-NP may be explored as an effective inhibitor
for hACE2-S complex. Furthermore, in vitro and in vivo studies will strengthen the use of these inhibitors as
suitable drug candidates against SARS-COV-2. Communicated by Ramaswamy H. Sarma
Collapse
Affiliation(s)
- Jitendra Subhash Rane
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Preeti Pandey
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Aroni Chatterjee
- Indian Council of Medical Research (ICMR)-Virus Research Laboratory, NICED, Kolkata, India
| | - Rajni Khan
- Motihari College of Engineering, Motihari, India
| | - Abhijeet Kumar
- Department of Chemistry, Mahatma Gandhi Central University, Motihari, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, India
| | - Shashikant Ray
- Department of Biotechnology, Mahatma Gandhi Central University, Motihari, India
| |
Collapse
|
18
|
Bhowmik D, Nandi R, Jagadeesan R, Kumar N, Prakash A, Kumar D. Identification of potential inhibitors against SARS-CoV-2 by targeting proteins responsible for envelope formation and virion assembly using docking based virtual screening, and pharmacokinetics approaches. INFECTION GENETICS AND EVOLUTION 2020; 84:104451. [PMID: 32640381 PMCID: PMC7335633 DOI: 10.1016/j.meegid.2020.104451] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023]
Abstract
WHO has declared the outbreak of COVID-19 as a public health emergency of international concern. The ever-growing new cases have called for an urgent emergency for specific anti-COVID-19 drugs. Three structural proteins (Membrane, Envelope and Nucleocapsid protein) play an essential role in the assembly and formation of the infectious virion particles. Thus, the present study was designed to identify potential drug candidates from the unique collection of 548 anti-viral compounds (natural and synthetic anti-viral), which target SARS-CoV-2 structural proteins. High-end molecular docking analysis was performed to characterize the binding affinity of the selected drugs-the ligand, with the SARS-CoV-2 structural proteins, while high-level Simulation studies analyzed the stability of drug-protein interactions. The present study identified rutin, a bioflavonoid and the antibiotic, doxycycline, as the most potent inhibitor of SARS-CoV-2 envelope protein. Caffeic acid and ferulic acid were found to inhibit SARS-CoV-2 membrane protein while the anti-viral agent's simeprevir and grazoprevir showed a high binding affinity for nucleocapsid protein. All these compounds not only showed excellent pharmacokinetic properties, absorption, metabolism, minimal toxicity and bioavailability but were also remain stabilized at the active site of proteins during the MD simulation. Thus, the identified lead compounds may act as potential molecules for the development of effective drugs against SARS-CoV-2 by inhibiting the envelope formation, virion assembly and viral pathogenesis.
Collapse
Affiliation(s)
- Deep Bhowmik
- Department of Microbiology, Assam University, Silchar 788011, Assam, India
| | - Rajat Nandi
- Department of Microbiology, Assam University, Silchar 788011, Assam, India
| | - Rahul Jagadeesan
- CAS in Crystallography and Biophysics, Guindy Campus, University of Madras, Chennai 600025, India
| | - Niranjan Kumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon 122413, India
| | - Diwakar Kumar
- Department of Microbiology, Assam University, Silchar 788011, Assam, India.
| |
Collapse
|
19
|
A review on the synthesis and applications of molecules as anticonvulsant drug agent candidates. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02595-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
20
|
Structure-based screening of novel lichen compounds against SARS Coronavirus main protease (Mpro) as potentials inhibitors of COVID-19. Mol Divers 2020; 25:1665-1677. [PMID: 32602074 PMCID: PMC7323881 DOI: 10.1007/s11030-020-10118-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022]
Abstract
The outbreak of SARS-CoV-2 and deaths caused by it all over the world have imposed great concern on the scientific community to develop potential drugs to combat Coronavirus disease-19 (COVID-19). In this regard, lichen metabolites may offer a vast reservoir for the discovery of antiviral drug candidates. Therefore, to find novel compounds against COVID-19, we created a library of 412 lichen compounds and subjected to virtual screening against the SARS-CoV-2 Main protease (Mpro). All the ligands were virtually screened, and 27 compounds were found to have high affinity with Mpro. These compounds were assessed for drug-likeness analysis where two compounds were found to fit well for redocking studies. Molecular docking, drug-likeness, X-Score, and toxicity analysis resulting in two lichen compounds, Calycin and Rhizocarpic acid with Mpro-inhibiting activity. These compounds were finally subjected to molecular dynamics simulation to compare the dynamics behavior and stability of the Mpro after ligand binding. The binding energy was calculated by MM-PBSA method to determine the intermolecular protein-ligand interactions. Our results showed that two compounds; Calycin and Rhizocarpic acid had the binding free energy of - 42.42 kJ mol/1 and - 57.85 kJ mol/1 respectively as compared to reference X77 (- 91.78 kJ mol/1). We concluded that Calycin and Rhizocarpic acid show considerable structural and pharmacological properties and they can be used as hit compounds to develop potential antiviral agents against SARS-CoV-2. These lichen compounds may be a suitable candidate for further experimental analysis.
Collapse
|
21
|
Mishra CB, Shalini S, Gusain S, Prakash A, Kumari J, Kumari S, Yadav AK, Lynn AM, Tiwari M. Development of novel N-(6-methanesulfonyl-benzothiazol-2-yl)-3-(4-substituted-piperazin-1-yl)-propionamides with cholinesterase inhibition, anti-β-amyloid aggregation, neuroprotection and cognition enhancing properties for the therapy of Alzheimer's disease. RSC Adv 2020; 10:17602-17619. [PMID: 35515597 PMCID: PMC9053591 DOI: 10.1039/d0ra00663g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/19/2020] [Indexed: 12/14/2022] Open
Abstract
A novel series of benzothiazole–piperazine hybrids were rationally designed, synthesized, and evaluated as multifunctional ligands against Alzheimer's disease (AD). The synthesized hybrid molecules illustrated modest to strong inhibition of acetylcholinesterase (AChE) and Aβ1-42 aggregation. Compound 12 emerged as the most potent hybrid molecule exhibiting balanced functions with effective, uncompetitive and selective inhibition against AChE (IC50 = 2.31 μM), good copper chelation, Aβ1-42 aggregation inhibition (53.30%) and disaggregation activities. Confocal laser scanning microscopy and TEM analysis also validate the Aβ fibril inhibition ability of this compound. Furthermore, this compound has also shown low toxicity and is capable of impeding loss of cell viability elicited by H2O2 neurotoxicity in SHSY-5Y cells. Notably, compound 12 significantly improved cognition and spatial memory against scopolamine-induced memory deficit in a mouse model. Hence, our results corroborate the multifunctional nature of novel hybrid molecule 12 against AD and it may be a suitable lead for further development as an effective therapeutic agent for therapy in the future. A novel series of benzothiazole–piperazine hybrids were rationally designed, synthesized, and evaluated as multifunctional ligands against Alzheimer's disease (AD).![]()
Collapse
Affiliation(s)
- Chandra Bhushan Mishra
- Dr. B. R. Ambedkar Centre for Biomedical Research
- University of Delhi
- New Delhi 110007
- India
| | - Shruti Shalini
- Dr. B. R. Ambedkar Centre for Biomedical Research
- University of Delhi
- New Delhi 110007
- India
| | - Siddharth Gusain
- Dr. B. R. Ambedkar Centre for Biomedical Research
- University of Delhi
- New Delhi 110007
- India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health (AIISH)
- Amity University Haryana
- Gurgaon-122413
- India
| | - Jyoti Kumari
- Dr. B. R. Ambedkar Centre for Biomedical Research
- University of Delhi
- New Delhi 110007
- India
| | - Shikha Kumari
- Dr. B. R. Ambedkar Centre for Biomedical Research
- University of Delhi
- New Delhi 110007
- India
| | - Anita Kumari Yadav
- Dr. B. R. Ambedkar Centre for Biomedical Research
- University of Delhi
- New Delhi 110007
- India
| | - Andrew M. Lynn
- School of Computational & Integrative Sciences
- Jawaharlal Nehru University
- New Delhi 110067
- India
| | - Manisha Tiwari
- Dr. B. R. Ambedkar Centre for Biomedical Research
- University of Delhi
- New Delhi 110007
- India
| |
Collapse
|
22
|
Kumar N, Srivastava R, Prakash A, Lynn AM. Structure-based virtual screening, molecular dynamics simulation and MM-PBSA toward identifying the inhibitors for two-component regulatory system protein NarL of Mycobacterium Tuberculosis. J Biomol Struct Dyn 2019; 38:3396-3410. [PMID: 31422761 DOI: 10.1080/07391102.2019.1657499] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The nitrate/nitrite response regulatory protein NarL belongs to the two-component regulatory system of Mycobacterium tuberculosis (MTB), plays a crucial role in anaerobic survival of mycobacteria in host. The absence of this protein in humans, makes it an attractive drug target for MTB treatment. However, the specific drug molecules targeting NarL are yet to be identified. In this study, we identified the promising drug candidates using structure based virtual screening of compounds from chemical libraries (ChEMBL and ZINC), followed by the extensive physicochemical properties analyses and molecular dynamics (MD) simulation. As the initial results, we obtained 4,754 bioactive compounds from ChEMBL having anti-tuberculosis activity which is finally narrowed down to the best 10 hits. A similar approach was applied to search for structurally similar compounds from ZINC data, corresponding to the top hits obtained from ChEMBL. Our collective results show that two compounds, ChEMBL509609 (Gscore - 5.054 kcal/mol, Xscore - 6.47 kcal/mol) and ZINC01843143 (Gscore - 5.114 kcal/mol, Xscore - 6.46 kcal/mol) having the best docking score and ADMET profile. The structural stability and dynamics of lead molecules at active site of NarL were examined using MD simulation and the binding free energies were estimated with MM-PBSA. Essential dynamics and MM-PBSA demonstrated that NarL-ChEMBL509609 complex remains the most stable during simulation of 100 ns with the higher binding free energy which may be a suitable candidate for further experimental analysis. AbbreviationsADMEAbsorption, Distribution, Metabolism, And ExcretionBCGBacillus Calmette-GuerinCNSCentral nervous systemDOTSDirectly observed treatment, short courseEDEssential dynamicsHIVHuman immunodeficiency virusHKHistidine kinaseHOAHuman oral absorptionHTVSHigh throughput virtual screeningIRRIIrritationMDMolecular dynamicsMDRMultidrug resistantMTBMycobacterium tuberculosisMUTMutagenicityMWMolecular weightPHOAPercentage of human oral absorptionREPReproductive developmentRgRadius of gyrationRMSDRoot mean square deviationRMSFRoot mean square fluctuationRO5Lipinski's rule of fiveRRResponse regulatorSPStandard precisionSPGStandard precision glideTBTuberculosisTCSTwo-component regulatory systemTDRTotally drug-resistantTUMOTumorigenicityWHOWorld health organizationXDRExtensively drug-resistantXPExtra precisionCommunicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Niranjan Kumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Srivastava
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University, Haryana, Gurgaon, India
| | - Andrew M Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
23
|
Abstract
INTRODUCTION Neuroinflammation has a critical role in brain disorders. Cyclooxygenase (COX) is one of the principal drug targets for the reduction of neuroinflammation; however, studies have yielded mixed results for COX-inhibitors in the treatment of diverse acute and chronic models of epilepsy. AREAS COVERED The article covers the effects of COX-inhibitors in epilepsy disorders. A considerable emphasis has been placed on the antiepileptic and 'disease-modifying' properties of COX-1 and COX-2 inhibitors in various preclinical epilepsy models. EXPERT OPINION The effect of COX-inhibitors on epilepsy is inconclusive. Studies have indicated beneficial effects in preclinical models; however, proconvulsant or no effects have also been observed. These molecules may have a bidirectional role with early neuroprotective and delayed neurotoxic effects. Further systematic preclinical studies to establish the use of COX-inhibitors in epilepsy are necessary.
Collapse
Affiliation(s)
- Ashish Dhir
- a Department of Neurology, School of Medicine , University of California, Davis , Sacramento , CA , USA
| |
Collapse
|
24
|
Rojas A, Chen D, Ganesh T, Varvel NH, Dingledine R. The COX-2/prostanoid signaling cascades in seizure disorders. Expert Opin Ther Targets 2018; 23:1-13. [PMID: 30484341 DOI: 10.1080/14728222.2019.1554056] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction:A robust neuroinflammatory response is a prevalent feature of multiple neurological disorders, including epilepsy and acute status epilepticus. One component of this neuroinflammatory reaction is the induction of cyclooxygenase-2 (COX-2), synthesis of several prostaglandins and endocannabinoid metabolites, and subsequent activation of prostaglandin and related receptors. Neuroinflammation mediated by COX-2 and its downstream effectors has received considerable attention as a potential target class to ameliorate the deleterious consequences of neurological injury. Areas covered: Here we describe the roles of COX-2 as a major inflammatory mediator. In addition, we discuss the receptors for prostanoids PGE2, prostaglandin D2, and PGF2α as potential therapeutic targets for inflammation-driven diseases. The consequences of prostanoid receptor activation after seizure activity are discussed with an emphasis on the utilization of small molecules to modulate prostanoid receptor activity. Expert opinion: Limited clinical trial experience is supportive but not definitive for a role of the COX signaling cascade in epileptogenesis. The cardiotoxicity associated with chronic coxib use, and the expectation that COX-2 inhibition will influence the levels of endocannabinoids, leukotrienes, and lipoxins as well as the prostaglandins and their endocannabinoid metabolite analogs, is shifting attention toward downstream synthases and receptors that mediate inflammation in the brain.
Collapse
Affiliation(s)
- Asheebo Rojas
- a Department of Pharmacology , Emory University School of Medicine , Atlanta , GA , USA
| | - Di Chen
- a Department of Pharmacology , Emory University School of Medicine , Atlanta , GA , USA
| | - Thota Ganesh
- a Department of Pharmacology , Emory University School of Medicine , Atlanta , GA , USA
| | - Nicholas H Varvel
- a Department of Pharmacology , Emory University School of Medicine , Atlanta , GA , USA
| | - Raymond Dingledine
- a Department of Pharmacology , Emory University School of Medicine , Atlanta , GA , USA
| |
Collapse
|