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Shi D, Liao N, Liu H, Gao W, Zhong S, Zheng C, Chen H, Xiao L, Zhu Y, Huang S, Zhang Y, Hu Y, Zheng Y, Ji J, Cheng J. Rapid Analysis of Compounds from Piperis Herba and Piperis Kadsurae Caulis and Their Differences Using High-Resolution Liquid-Mass Spectrometry and Molecular Network Binding Antioxidant Activity. Molecules 2024; 29:439. [PMID: 38257353 PMCID: PMC10821392 DOI: 10.3390/molecules29020439] [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: 01/04/2024] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
There is a serious mixing of Piperis Herba and Piperis Kadsurae Caulis in various parts of China due to the similar traits of lianas, and there is a lack of systematic research on the compound and activity evaluation of the two. Likewise, the differences in compounds brought about by the distribution of origin also need to be investigated. In this study, high-resolution liquid-mass spectrometry (UPLC-Q-Zeno-TOF-MS/MS) was used to analyze samples of Piperis Herba from five origins and Piperis Kadsurae Caulis from five origins, with three batches collected from each origin. The compounds were identified based on precise molecular weights, secondary fragments, and an online database combined with node-to-node associations of the molecular network. The t-test was used to screen and analyze the differential compounds between the two. Finally, the preliminary evaluation of antioxidant activity of the two herbs was carried out using DPPH and ABTS free radical scavenging assays. The results showed that a total of 72 compounds were identified and deduced in the two Chinese medicines. These compounds included 54 amide alkaloids and 18 other compounds, such as flavonoid glycosides. The amide alkaloids among them were then classified, and the cleavage pathways in positive ion mode were summarized. Based on the p-value of the t-test, 32 differential compounds were screened out, and it was found that the compounds of Piperis Herba were richer and possessed a broader spectrum of antioxidant activity, thus realizing a multilevel distinction between Piperis Herba and Piperis Kadsurae Caulis. This study provides a preliminary reference for promoting standardization and comprehensive quality research of the resources of Piperis Herba using Piperis Kadsurae Caulis as a reference.
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Affiliation(s)
- Dezhi Shi
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
- Jiangsu Province Engineering Research Center of Classical Prescription, Nanjing 210023, China
| | - Nanxi Liao
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
- Jiangsu Province Engineering Research Center of Classical Prescription, Nanjing 210023, China
| | - Hualan Liu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
- Jiangsu Province Engineering Research Center of Classical Prescription, Nanjing 210023, China
| | - Wufeng Gao
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
- Jiangsu Province Engineering Research Center of Classical Prescription, Nanjing 210023, China
| | - Shaohui Zhong
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
- Jiangsu Province Engineering Research Center of Classical Prescription, Nanjing 210023, China
| | - Chao Zheng
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
- Jiangsu Province Engineering Research Center of Classical Prescription, Nanjing 210023, China
| | - Haijie Chen
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
| | - Lianlian Xiao
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
- Jiangsu Province Engineering Research Center of Classical Prescription, Nanjing 210023, China
| | - Yubo Zhu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
- Jiangsu Province Engineering Research Center of Classical Prescription, Nanjing 210023, China
| | - Shiwen Huang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
| | - Yunyu Zhang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
- Jiangsu Province Engineering Research Center of Classical Prescription, Nanjing 210023, China
| | - Yang Hu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
- Jiangsu Province Engineering Research Center of Classical Prescription, Nanjing 210023, China
| | - Yunfeng Zheng
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
- Jiangsu Province Engineering Research Center of Classical Prescription, Nanjing 210023, China
| | - Jing Ji
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
- Jiangsu Province Engineering Research Center of Classical Prescription, Nanjing 210023, China
| | - Jianming Cheng
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; (D.S.); (N.L.); (H.L.); (W.G.); (S.Z.); (C.Z.); (H.C.); (L.X.); (Y.Z.); (S.H.); (Y.Z.); (Y.H.); (Y.Z.)
- Jiangsu Province Engineering Research Center of Classical Prescription, Nanjing 210023, China
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Phytochemistry and Pharmacology of Medicinal Plants Used by the Tenggerese Society in Java Island of Indonesia. Molecules 2022; 27:molecules27217532. [DOI: 10.3390/molecules27217532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
The archipelagic country of Indonesia is inhabited by 300 ethnic groups, including the indigenous people of Tengger. Based on the reported list of medicinal plants used by the Tengger community, we have reviewed each of them for their phytochemical constituents and pharmacological activities. Out of a total of 41 medicinal plants used by the Tengerrese people, 33 species were studied for their phytochemical and pharmacological properties. More than 554 phytochemicals with diverse molecular structures belonging to different chemical classes including flavonoids, terpenoids, saponins and volatiles were identified from these studied 34 medicinal plants. Many of these medicinal plants and their compounds have been tested for various pharmacological activities including anti-inflammatory, antimicrobial, wound healing, headache, antimalarial and hypertension. Five popularly used medicinal plants by the healers were Garcinia mangostana, Apium graveolens, Cayratia clematidea, Drymocallis arguta and Elaeocarpus longifolius. Only A. graviolens were previously studied, with the outcomes supporting the pharmacological claims to treat hypertension. Few unexplored medicinal plants are Physalis lagascae, Piper amplum, Rosa tomentosa and Tagetes tenuifolia, and they present great potential for biodiscovery and drug lead identification.
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Mukherjee N, Banerjee S, Amin SA, Jha T, Datta S, Das Saha K. Host P2X 7R-p 38MAPK axis mediated intra-macrophage leishmanicidal activity of Spergulin-A. Exp Parasitol 2022; 241:108365. [PMID: 36007587 DOI: 10.1016/j.exppara.2022.108365] [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: 04/04/2022] [Revised: 07/14/2022] [Accepted: 08/18/2022] [Indexed: 11/04/2022]
Abstract
Current drugs are inefficient for the treatment of visceral leishmaniasis an immunosuppressive ailment caused by Leishmania donovani. Regrettably, there is no plant-origin antileishmanial drug present. P2X7R is constitutively present on macrophage surfaces and can be a putative therapeutic target in intra-macrophage pathogens with function attributes towards inflammation, host cell apoptosis, altered redox, and phagolysosomal maturation by activating p38MAPK. Here we demonstrated that the initial interaction of Spergulin-A (Sp A), a triterpenoid saponin with RAW 264.7 macrophages was mediated through P2X7R involving the signaling cascade intermediates Ca++, p38MAPK, and NF-κβ. Phospho (P)-p38MAPK involvement is shown to have specific and firm importance in leishmanial killing with increased NF-κβp65. Phago-lysosomal maturation by Sp A also campaigns for another contribution of P2X7R. In vivo evaluation of the anti-leishmanial activity of Sp A was monitored through expression analyses of P2X7R, P-p38MAPK, and NF-κβp65 in murine spleen and bone-marrow macrophages and supported Sp A being a natural compound of leishmanicidal functions which acted through the P2X7R-p38MAPK axis.
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Affiliation(s)
- Niladri Mukherjee
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, India; Techno India University, EM-4, Sector V, Salt Lake, Kolkata, 700091, West Bengal, India.
| | - Saswati Banerjee
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, India
| | - Sk Abdul Amin
- Natural Science Laboratory, Department of Pharmaceutical Technology, Division of Medicinal & Pharmaceutical Chemistry, P. O. Box 17020, Jadavpur University, Kolkata, 700032, India
| | - Tarun Jha
- Natural Science Laboratory, Department of Pharmaceutical Technology, Division of Medicinal & Pharmaceutical Chemistry, P. O. Box 17020, Jadavpur University, Kolkata, 700032, India
| | - Sriparna Datta
- Department of Chemical Technology, University of Calcutta, Kolkata, 700009, India
| | - Krishna Das Saha
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, India.
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Ahmed S, Ali MC, Ruma RA, Mahmud S, Paul GK, Saleh MA, Alshahrani MM, Obaidullah AJ, Biswas SK, Rahman MM, Rahman MM, Islam MR. Molecular Docking and Dynamics Simulation of Natural Compounds from Betel Leaves ( Piper betle L.) for Investigating the Potential Inhibition of Alpha-Amylase and Alpha-Glucosidase of Type 2 Diabetes. Molecules 2022; 27:molecules27144526. [PMID: 35889399 PMCID: PMC9316265 DOI: 10.3390/molecules27144526] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022] Open
Abstract
Piper betle L. is widely distributed and commonly used medicinally important herb. It can also be used as a medication for type 2 diabetes patients. In this study, compounds of P. betle were screened to investigate the inhibitory action of alpha-amylase and alpha-glucosidase against type 2 diabetes through molecular docking, molecular dynamics simulation, and ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis. The molecule apigenin-7-O-glucoside showed the highest binding affinity among 123 (one hundred twenty-three) tested compounds. This compound simultaneously bound with the two-target proteins alpha-amylase and alpha-glucosidase, with high molecular mechanics-generalized born surface area (MM/GBSA) values (ΔG Bind = -45.02 kcal mol-1 for alpha-amylase and -38.288 for alpha-glucosidase) compared with control inhibitor acarbose, which had binding affinities of -36.796 kcal mol-1 for alpha-amylase and -29.622 kcal mol-1 for alpha-glucosidase. The apigenin-7-O-glucoside was revealed to be the most stable molecule with the highest binding free energy through molecular dynamics simulation, indicating that it could compete with the inhibitors' native ligand. Based on ADMET analysis, this phytochemical exhibited a wide range of physicochemical, pharmacokinetic, and drug-like qualities and had no significant side effects, making them prospective drug candidates for type 2 diabetes. Additional in vitro, in vivo, and clinical investigations are needed to determine the precise efficacy of drugs.
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Affiliation(s)
- Sabbir Ahmed
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
| | - Md Chayan Ali
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
| | - Rumana Akter Ruma
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
| | - Shafi Mahmud
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia;
| | - Gobindo Kumar Paul
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (G.K.P.); (M.A.S.)
| | - Md Abu Saleh
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (G.K.P.); (M.A.S.)
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia;
| | - Ahmad J. Obaidullah
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sudhangshu Kumar Biswas
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
| | - Md Mafizur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
- Correspondence:
| | - Md Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
| | - Md Rezuanul Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.A.); (M.C.A.); (R.A.R.); (S.K.B.); (M.M.R.); (M.R.I.)
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Biswas P, Anand U, Saha SC, Kant N, Mishra T, Masih H, Bar A, Pandey DK, Jha N, Majumder M, Das N, Gadekar V, Shekhawat MS, Kumar M, Radha, Proćków J, de la Lastra JMP, Dey A. Betelvine (Piper betle L.): A comprehensive insight into its ethnopharmacology, phytochemistry, and pharmacological, biomedical and therapeutic attributes. J Cell Mol Med 2022; 26:3083-3119. [PMID: 35502487 PMCID: PMC9170825 DOI: 10.1111/jcmm.17323] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/28/2022] [Accepted: 03/24/2022] [Indexed: 12/11/2022] Open
Abstract
Piper betle L. (synonym: Piper betel Blanco), or betel vine, an economically and medicinally important cash crop, belongs to the family Piperaceae, often known as the green gold. The plant can be found all over the world and is cultivatedprimarily in South East Asian countries for its beautiful glossy heart-shaped leaves, which are chewed or consumed as betelquidand widely used in Chinese and Indian folk medicine, as carminative, stimulant,astringent, against parasitic worms, conjunctivitis, rheumatism, wound, etc., andis also used for religious purposes. Hydroxychavicol is the most important bioactive compound among the wide range of phytoconstituents found in essential oil and extracts. The pharmacological attributes of P. betle are antiproliferation, anticancer, neuropharmacological, analgesic, antioxidant, antiulcerogenic, hepatoprotective, antifertility, antibacterial, antifungal and many more. Immense attention has been paid to nanoformulations and their applications. The application of P. betle did not show cytotoxicity in preclinical experiments, suggesting that it could serve as a promising therapeutic candidate for different diseases. The present review comprehensively summarizes the botanical description, geographical distribution, economic value and cultivation, ethnobotanical uses, preclinical pharmacological properties with insights of toxicological, clinical efficacy, and safety of P. betle. The findings suggest that P. betle represents an orally active and safe natural agent that exhibits great therapeutic potential for managing various human medical conditions. However, further research is needed to elucidate its underlying molecular mechanisms of action, clinical aspects, structure-activity relationships, bioavailability and synergistic interactions with other drugs.
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Affiliation(s)
- Protha Biswas
- Department of Life SciencesPresidency UniversityKolkataWest BengalIndia
| | - Uttpal Anand
- Department of Life SciencesBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Suchismita Chatterjee Saha
- Department of ZoologyNabadwip Vidyasagar College (Affiliated to the University of Kalyani)NabadwipWest BengalIndia
| | - Nishi Kant
- Department of BiotechnologySchool of Health and Allied ScienceARKA Jain UniversityJamshedpurJharkhandIndia
| | - Tulika Mishra
- Department of BotanyDeen Dayal Upadhyay Gorakhpur UniversityGorakhpurUttar PradeshIndia
| | - Harison Masih
- Department of Industrial MicrobiologyJacob Institute of Biotechnology and BioengineeringSam Higginbottom University of Agriculture, Technology and SciencesPrayagrajUttar PradeshIndia
| | - Ananya Bar
- Department of ZoologyWilson College (Affiliated to University of Mumbai)MumbaiMaharashtraIndia
| | | | - Niraj Kumar Jha
- Department of BiotechnologySchool of Engineering & TechnologySharda UniversityGreater NoidaUttar PradeshIndia
| | - Madhumita Majumder
- Department of BotanyRaidighi College (Affiliated to University of Calcutta)RaidighiWest BengalIndia
| | - Neela Das
- Department of BotanyRishi Bankim Chandra College (Affiliated to the West Bengal State University)NaihatiWest BengalIndia
| | - Vijaykumar Shivaji Gadekar
- Zoology DepartmentSangola College (Affiliated to Punyashlok Ahilyadevi Holkar Solapur University)SolapurMaharashtraIndia
| | - Mahipal S. Shekhawat
- Plant Biotechnology UnitKanchi Mamunivar Government Institute for Postgraduate Studies and ResearchPuducherryIndia
| | - Manoj Kumar
- Chemical and Biochemical Processing DivisionICAR ‐ Central Institute for Research on Cotton TechnologyMumbaiMaharashtraIndia
| | - Radha
- School of Biological and Environmental SciencesShoolini University of Biotechnology and Management SciencesSolanHimachal PradeshIndia
| | - Jarosław Proćków
- Department of Plant BiologyInstitute of Environmental BiologyWrocław University of Environmental and Life SciencesWrocławPoland
| | - José M. Pérez de la Lastra
- Instituto de Productos Naturales y Agrobiología (IPNA)Consejo Superior de Investigaciones científicas (CSIS)Santa Cruz de TenerifeSpain
| | - Abhijit Dey
- Department of Life SciencesPresidency UniversityKolkataWest BengalIndia
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Kumari P, Pradhan B, Koromina M, Patrinos GP, Steen KV. Discovery of new drug indications for COVID-19: A drug repurposing approach. PLoS One 2022; 17:e0267095. [PMID: 35609015 PMCID: PMC9129022 DOI: 10.1371/journal.pone.0267095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/03/2022] [Indexed: 11/19/2022] Open
Abstract
Motivation
The outbreak of coronavirus health issues caused by COVID-19(SARS-CoV-2) creates a global threat to public health. Therefore, there is a need for effective remedial measures using existing and approved therapies with proven safety measures has several advantages. Dexamethasone (Pubchem ID: CID0000005743), baricitinib(Pubchem ID: CID44205240), remdesivir (PubchemID: CID121304016) are three generic drugs that have demonstrated in-vitro high antiviral activity against SARS-CoV-2. The present study aims to widen the search and explore the anti-SARS-CoV-2 properties of these potential drugs while looking for new drug indications with optimised benefits via in-silico research.
Method
Here, we designed a unique drug-similarity model to repurpose existing drugs against SARS-CoV-2, using the anti-Covid properties of dexamethasone, baricitinib, and remdesivir as references. Known chemical-chemical interactions of reference drugs help extract interactive compounds withimprovedanti-SARS-CoV-2 properties. Here, we calculated the likelihood of these drug compounds treating SARS-CoV-2 related symptoms using chemical-protein interactions between the interactive compounds of the reference drugs and SARS-CoV-2 target genes. In particular, we adopted a two-tier clustering approach to generate a drug similarity model for the final selection of potential anti-SARS-CoV-2 drug molecules. Tier-1 clustering was based on t-Distributed Stochastic Neighbor Embedding (t-SNE) and aimed to filter and discard outlier drugs. The tier-2 analysis incorporated two cluster analyses performed in parallel using Ordering Points To Identify the Clustering Structure (OPTICS) and Hierarchical Agglomerative Clustering (HAC). As a result, itidentified clusters of drugs with similar actions. In addition, we carried out a docking study for in-silico validation of top candidate drugs.
Result
Our drug similarity model highlighted ten drugs, including reference drugs that can act as potential therapeutics against SARS-CoV-2. The docking results suggested that doxorubicin showed the least binding energy compared to reference drugs. Their practical utility as anti-SARS-CoV-2 drugs, either individually or in combination, warrants further investigation.
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Affiliation(s)
- Priyanka Kumari
- GIGA-R Medical Genomics - BIO3 Systems Genomics, University of Liège, Liège, Belgium
- Laboratory of Pharmaceutical Analytical Chemistry, CIRM, University of Liège, Liège, Belgium
- * E-mail: (PK); (KVS)
| | - Bikram Pradhan
- Indian Space Research Organisation (ISRO) Headquarters, Bengaluru, India
| | - Maria Koromina
- University of Patras, School of Health Sciences, Department of Pharmacy, Patras, Greece
| | - George P. Patrinos
- University of Patras, School of Health Sciences, Department of Pharmacy, Patras, Greece
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, UAE
- Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University, Al Ain, UAE
| | - Kristel Van Steen
- GIGA-R Medical Genomics - BIO3 Systems Genomics, University of Liège, Liège, Belgium
- Department of Human Genetics - BIO3 Systems Medicine, University of Leuven, Leuven, Belgium
- * E-mail: (PK); (KVS)
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8
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San TT, Wang YH, Hu DB, Yang J, Zhang DD, Xia MY, Yang XF, Yang YP. A new sesquineolignan and four new neolignans isolated from the leaves of Piper betle, a traditional medicinal plant in Myanmar. Bioorg Med Chem Lett 2020; 31:127682. [PMID: 33207281 DOI: 10.1016/j.bmcl.2020.127682] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/04/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022]
Abstract
One new sesquineolignan, piperneolignan A (1), four new neolignans, piperneolignans B-E (2-5), and eight known compounds were isolated from the leaves of Piper betle (Piperaceae) collected from Myanmar. These new structures were determined by analysis of MS and NMR data, and the absolute configuration of piperneolignan A was elucidated by electronic circular dichroism (ECD) calculations. Piperneolignan A (1), piperneolignan B (2), hydroxychavicol (6), p-hydroxycinnamaldehyde (10), and diallylcatechol (13) possessed anti-inflammatory activity against nitric oxide (NO) production in lipopolysaccharide (LPS)-activated murine macrophage RAW 264.7 cells with IC50 values of 9.87, 45.94, 4.80, 26.40, and 40.45 μM, respectively, compared with the positive control NG-monomethyl-l-arginine (l-NMMA, IC50 = 33.84 μM). The two hydroxy groups in the structure of hydroxychavicol are essential for activity, and dimerization or trimerization of hydroxychavicol decreases activity.
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Affiliation(s)
- Thae Thae San
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar; Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yue-Hu Wang
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar; Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Dong-Bao Hu
- School of Chemical Biology and Environment, Yuxi Normal University, Yuxi 653100, People's Republic of China
| | - Jun Yang
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar; Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Dong-Dong Zhang
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar; Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Meng-Yuan Xia
- Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Xue-Fei Yang
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar; Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China.
| | - Yong-Ping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China.
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9
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Zivkovic M, Zlatanovic M, Zlatanovic N, Golubović M, Veselinović AM. The Application of the Combination of Monte Carlo Optimization Method based QSAR Modeling and Molecular Docking in Drug Design and Development. Mini Rev Med Chem 2020; 20:1389-1402. [DOI: 10.2174/1389557520666200212111428] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 01/18/2023]
Abstract
In recent years, one of the promising approaches in the QSAR modeling Monte Carlo optimization
approach as conformation independent method, has emerged. Monte Carlo optimization has
proven to be a valuable tool in chemoinformatics, and this review presents its application in drug discovery
and design. In this review, the basic principles and important features of these methods are discussed
as well as the advantages of conformation independent optimal descriptors developed from the
molecular graph and the Simplified Molecular Input Line Entry System (SMILES) notation compared
to commonly used descriptors in QSAR modeling. This review presents the summary of obtained results
from Monte Carlo optimization-based QSAR modeling with the further addition of molecular
docking studies applied for various pharmacologically important endpoints. SMILES notation based
optimal descriptors, defined as molecular fragments, identified as main contributors to the increase/
decrease of biological activity, which are used further to design compounds with targeted activity
based on computer calculation, are presented. In this mini-review, research papers in which molecular
docking was applied as an additional method to design molecules to validate their activity further,
are summarized. These papers present a very good correlation among results obtained from Monte
Carlo optimization modeling and molecular docking studies.
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Affiliation(s)
| | | | | | - Mladjan Golubović
- Clinic for Anesthesiology and Intensive Care, Clinical Center Nis, Nis, Serbia
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10
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Nepali K, Chang TY, Lai MJ, Hsu KC, Yen Y, Lin TE, Lee SB, Liou JP. Purine/purine isoster based scaffolds as new derivatives of benzamide class of HDAC inhibitors. Eur J Med Chem 2020; 196:112291. [PMID: 32325365 DOI: 10.1016/j.ejmech.2020.112291] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/17/2020] [Accepted: 03/27/2020] [Indexed: 12/12/2022]
Abstract
This study reports the design, synthesis and evaluation of a series of histone deacetylase (HDAC) inhibitors containing purine/purine isoster as a capping group and an N-(2-aminophenyl)-benzamide unit. In vitro cytotoxicity studies reveal that benzamide 14 suppressed the growth of triple-negative breast cancer cells MDA-MB-231 (IC50 = 1.48 μM), MDA-MB-468 (IC50 = 0.65 μM), and liver cancer cells HepG2 (IC50 = 2.44 μM), better than MS-275 (5) and Chidamide (6). Compared to the well-known HDAC inhibitor SAHA, 14 showed a higher toxicity (IC50 = 0.33 μM) in three leukemic cell lines, K-562, KG-1 and THP-1. Moreover, 14 was found to be equally virulent in the HDAC-sensitive and -resistant gastric cell lines, YCC11 and YCC3/7, respectively, indicating the potential of 14 to overcome HDACi resistance. Furthermore, substantial inhibitory effects more pronounced than MS-275 (5) and Chidamide (6) were displayed by 14 towards HDAC1, 2 and 3 isoforms with IC50 values of 0.108, 0.585 and 0.563 μM respectively. Compound 14 also exhibited a potent antitumor efficacy in human MDA-MB-231 breast cancer xenograft mouse model, providing a potential lead for the development of anticancer agents.
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Affiliation(s)
- Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taiwan
| | - Ting-Yu Chang
- Ph.D. Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taiwan; Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taiwan; Graduate Institute of Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Mei-Jung Lai
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taiwan
| | - Kai-Cheng Hsu
- Ph.D. Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taiwan; TMU Biomedical Commercialization Center, Taipei Medical University, Taiwan; Graduate Institute of Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Yun Yen
- Graduate Institute of Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Tony Eight Lin
- Graduate Institute of Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Sung-Bau Lee
- Ph.D. Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taiwan; Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taiwan.
| | - Jing-Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taiwan; Ph.D. Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taiwan; TMU Biomedical Commercialization Center, Taipei Medical University, Taiwan; School of Pharmacy, National Defense Medical Center, Taipei, Taiwan.
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11
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Bhardwaj B, Baidya ATK, Amin SA, Adhikari N, Jha T, Gayen S. Insight into structural features of phenyltetrazole derivatives as ABCG2 inhibitors for the treatment of multidrug resistance in cancer. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2019; 30:457-475. [PMID: 31157558 DOI: 10.1080/1062936x.2019.1615545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
ABCG2 is the principal ABC transporter involved in the multidrug resistance of breast cancer. Looking at the current demand in the development of ABCG2 inhibitors for the treatment of multidrug-resistant cancer, we have explored structural requirements of phenyltetrazole derivatives for ABCG2 inhibition by combining classical QSAR, Bayesian classification modelling and molecular docking studies. For classical QSAR, structural descriptors were calculated from the free software tool PaDEL-descriptor. Stepwise multiple linear regression (SMLR) was used for model generation. A statistically significant model was generated and validated with different parameters (For training set: r = 0.825; Q2 = 0.570 and for test set: r = 0.894, r2pred = 0.783). The predicted model was found to satisfy the Golbraikh and Trospha criteria for model acceptability. Bayesian classification modelling was also performed (ROC scores were 0.722 and 0.767 for the training and test sets, respectively). Finally, the binding interactions of phenyltetrazole type inhibitor with the ABCG2 receptor were mapped with the help of molecular docking study. The result of the docking analysis is aligned with the classical QSAR and Bayesian classification studies. The combined modelling study will guide the medicinal chemists to act faster in the drug discovery of ABCG2 inhibitors for the management of resistant breast cancer.
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Affiliation(s)
- B Bhardwaj
- a Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr. Harisingh Gour University , Madhya Pradesh , India
| | - A T K Baidya
- a Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr. Harisingh Gour University , Madhya Pradesh , India
| | - S A Amin
- b Natural Science Laboratory, Department of Pharmaceutical Technology, Division of Medicinal & Pharmaceutical Chemistry , Jadavpur University , Kolkata , India
| | - N Adhikari
- b Natural Science Laboratory, Department of Pharmaceutical Technology, Division of Medicinal & Pharmaceutical Chemistry , Jadavpur University , Kolkata , India
| | - T Jha
- b Natural Science Laboratory, Department of Pharmaceutical Technology, Division of Medicinal & Pharmaceutical Chemistry , Jadavpur University , Kolkata , India
| | - S Gayen
- a Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr. Harisingh Gour University , Madhya Pradesh , India
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12
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Kostić T, Deljanin Ilić M, Perišić Z, Milić D, Đorđević M, Golubović M, Koraćević G, Šalinger Martinović S, Ćirić Zdravković S, Živić S, Lazarević M, Stanojević D, Dakić S, Lilić J, Veselinović A. Design and development of novel therapeutics for coronary heart disease treatment based on cholesteryl ester transfer protein inhibition - in silico approach. J Biomol Struct Dyn 2019; 38:2304-2313. [PMID: 31215331 DOI: 10.1080/07391102.2019.1630319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Cholesteryl ester transfer protein (CETP) belongs to the group of enzymes which inhibition have the application in the treatment of cardiovascular diseases. This study presents QSAR modeling for a set of compounds acting as CETP inhibitors based on the Monte Carlo optimization with SMILES notation and molecular graph-based descriptors, and field-based 3D modeling. A 3D QSAR model was developed for one random split into the training and test sets, whereas conformation independent QSAR models were developed for three random splits, with the results suggesting there is an excellent correlation between them. Various statistical approaches were used to assess the statistical quality of the developed models, including robustness and predictability, and the obtained results were very good. This study used a novel statistical metric known as the index of ideality of correlation for the final assessment of the model, and the results that were obtained suggested that the model was good. Also, molecular fragments which account for the increases and/or decreases of a studied activity were defined and then used for the computer-aided design of new compounds as potential CETP inhibitors. The final assessment of the developed QSAR model and designed inhibitors was done using molecular docking, which revealed an excellent correlation with the results from QSAR modeling.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tomislav Kostić
- Clinic for Cardiovascular Disease, Clinical Center Nis, Nis, Serbia
| | - Marina Deljanin Ilić
- Institute for Cardiovascular Prevention and Rehabilitation Niska Banja, Nis, Serbia
| | - Zoran Perišić
- Clinic for Cardiovascular Disease, Clinical Center Nis, Nis, Serbia
| | - Dragan Milić
- Clinic for Cardiovascular Surgery, Clinical Center Nis, Nis, Serbia
| | - Miodrag Đorđević
- Clinic for Endocrine Surgery and Breast Surgery, Clinical Center Nis, Nis, Serbia
| | - Mladjan Golubović
- Clinic for Anesthesiology and Intensive Care, Clinical Center Nis, Nis, Serbia
| | - Goran Koraćević
- Clinic for Cardiovascular Disease, Clinical Center Nis, Nis, Serbia
| | | | | | - Saša Živić
- Clinic for Cardiovascular Surgery, Clinical Center Nis, Nis, Serbia
| | - Milan Lazarević
- Clinic for Cardiovascular Surgery, Clinical Center Nis, Nis, Serbia
| | | | - Sonja Dakić
- Clinic for Cardiovascular Disease, Clinical Center Nis, Nis, Serbia
| | - Jelena Lilić
- Clinic for Anesthesiology and Intensive Care, Clinical Center Nis, Nis, Serbia
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13
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Zeb A, Son M, Yoon S, Kim JH, Park SJ, Lee KW. Computational Simulations Identified Two Candidate Inhibitors of Cdk5/p25 to Abrogate Tau-associated Neurological Disorders. Comput Struct Biotechnol J 2019; 17:579-590. [PMID: 31073393 PMCID: PMC6495220 DOI: 10.1016/j.csbj.2019.04.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/14/2019] [Accepted: 04/17/2019] [Indexed: 01/26/2023] Open
Abstract
Deregulation of Cdk5 is a hallmark in neurodegenerative diseases and its complex with p25 forms Cdk5/p25, thereby causes severe neuropathological insults. Cdk5/p25 abnormally phosphorylates tau protein, and induces tau-associated neurofibrillary tangles in neurological disorders. Therefore, the pharmacological inhibition of Cdk5/p25 alleviates tau-associated neurological disorders. Herein, computational simulations probed two candidate inhibitors of Cdk5/p25. Structure-based pharmacophore investigated the essential complementary chemical features of ATP-binding site of Cdk5 in complex with roscovitine. Resultant pharmacophore harbored polar interactions with Cys83 and Asp86 residues and non-polar interactions with Ile10, Phe80, and Lys133 residues of Cdk5. The chemical space of selected pharmacophore was comprised of two hydrogen bond donors, one hydrogen bond acceptor, and three hydrophobic features. Decoy test validation of pharmacophore obtained highest Guner-Henry score (0.88) and enrichment factor score (7.23). The screening of natural product drug-like databases by validated pharmacophore retrieved 1126 compounds as candidate inhibitors of Cdk5/p25. The docking of candidate inhibitors filtered 10 molecules with docking score >80.00 and established polar and non-polar interactions with the ATP-binding site residues of Cdk5/p25. Finally, molecular dynamics simulation and binding free energy analyses identified two candidate inhibitors of Cdk5/p25. During 30 ns simulation, the candidate inhibitors established <3.0 Å root mean square deviation and stable hydrogen bond interactions with the ATP-binding site residues of Cdk5/p25. The final candidate inhibitors obtained lowest binding free energies of -122.18 kJ/mol and - 117.26 kJ/mol with Cdk5/p25. Overall, we recommend two natural product candidate inhibitors to target the pharmacological inhibition of Cdk5/p25 in tau-associated neurological disorders.
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Key Words
- 2D, Two-dimentional
- 3D, Three-dimentional
- AD, Alzheimer's disease
- ADMET, Absorption, distribution, metabolism, excretion, and toxicity
- ASP, Astex statistical potential
- Aβ, Amyloid beta
- BBB, Blood-brain barrier
- CGMC, Cyclin-dependent kinases, mitogen-activated protein kinases, glycogen synthase kinases, and Cdk-like kinases
- Cdk5, Cyclin-dependent kinase 5
- Cdk5/p25 inhibitors
- Cdks, Cyclin-dependent kinases
- DS, Discovery Studio
- EF, Enrichment factor
- GA, Genetic algorithm
- GFA, Genetic Function Approximation
- GH, Guner-Henry
- GOLD, Genetic optimization of ligand docking
- GROMACS, Groningen Machine for Chemical Simulation
- H-bond, Hydrogen bond
- HBA, Hydrogen bond acceptor
- HBD, Hydrogen bond donor
- HD, Hungtington's disease
- HYP, Hydrophobic
- IBS, InterBioScreen
- K, kelvin
- MD, Molecular dynamics
- MPTP, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine
- Molecular docking
- Molecular dynamics simulation
- NPT, Number particle, pressure, and temperature
- NVT, Number of particles, volume, and temperature
- P5, A 24-residues mimetic peptide of p35
- PD, Parkinson's disease
- PDB, Protein databank
- PLP, Piecewise linear potential
- PME, Particle mesh ewald
- RMSD, Root mean square deviation
- ROF, Rule of five
- Structure-based pharmacophore modeling
- TAT, Twin-arginine targeting
- TIP3P, Transferable intermolecular potential with 3 points
- Tau-pathogenesis
- ZNPD, Zinc Natural Product Database
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Affiliation(s)
- Amir Zeb
- Division of Life Science, Division of Applied Life Sciences (BK21 Plus), Research Institute of Natural Sciences (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Gyeongnam, Republic of Korea
| | - Minky Son
- Division of Life Science, Division of Applied Life Sciences (BK21 Plus), Research Institute of Natural Sciences (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Gyeongnam, Republic of Korea
| | - Sanghwa Yoon
- Division of Life Science, Division of Applied Life Sciences (BK21 Plus), Research Institute of Natural Sciences (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Gyeongnam, Republic of Korea
| | - Ju Hyun Kim
- Department of Chemistry (BK21 Plus), Research Institute of Natural Science (RINS), Geyongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Gyeongnam, Republic of Korea
| | - Seok Ju Park
- Department of Internal Medicine, College of Medicine, Busan Paik Hospital, Inje University, Busan 47392, Republic of Korea
| | - Keun Woo Lee
- Division of Life Science, Division of Applied Life Sciences (BK21 Plus), Research Institute of Natural Sciences (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Gyeongnam, Republic of Korea
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14
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Zivkovic M, Zlatanovic M, Zlatanovic N, Golubović M, Veselinović AM. Development of novel therapeutics for glaucoma filtration surgery based on transforming growth factor-β receptor 1 inhibition. NEW J CHEM 2019. [DOI: 10.1039/c9nj05393j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
QSAR modeling with computer-aided drug design was used for the in silico development of novel therapeutics for glaucoma filtration surgery.
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Affiliation(s)
- Maja Zivkovic
- Faculty of Medicine
- Department of Ophthalmology
- University of Nis
- Nis
- Serbia
| | | | | | - Mladjan Golubović
- Clinic for Anesthesiology and Intensive Care
- Clinical Center Nis
- Nis
- Serbia
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15
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Bhattacharya P, Saha A, Basak S. Discovery of nano-piperolactam A: A nonsteroidal contraceptive lead acting through down-regulation of interleukins. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 18:347-358. [PMID: 30412768 DOI: 10.1016/j.nano.2018.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/16/2018] [Accepted: 10/25/2018] [Indexed: 10/27/2022]
Abstract
Elevated serum interleukins (IL-6, IL-1β) over baseline concentration help in blastocyst adhesion to the uterine endometrium in the early phase of pregnancy. A nano PLA (Piperolactam A)-HPBCD (2-hydroxy-propyl-β-cyclodextrin) inclusion complex was developed as an interleukin down-regulator that exhibited 100% anti-implantation activity in rodents at a dose as low as 2.5-5.0 mg/kg. On metabolomics study, among major glyco-lipo-protein metabolites, only serum low-density lipoprotein (LDL) or very low-density lipoprotein (VLDL) levels revealed alteration by the formulation. Administration of PLA-HPBCD did not cause changes in serum estrogen and progesterone levels. However, IL-6 and IL-1β failed to increase post PLA-HPBCD administration; hence, it is assumed to be the mode of the drug's abortifacient action. In addition, absence of signs of either acute or chronic toxicity suggests the formulation was considerably non-toxic. Therefore, the nano-PLA conjugate promises as a non-steroidal contraceptive lead apart from ormeloxifene, the only non-steroidal anti-fertility agent currently available globally.
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Affiliation(s)
| | - Achintya Saha
- Department of Chemical Technology, University of Calcutta, Kolkata, India
| | - Souvik Basak
- Dr. B.C. Roy College of Pharmacy and Allied Health Sciences, Durgapur, WB, India.
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16
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Molecular modeling of non-covalent binding of Ligustrum lucidum secoiridoid glucosides to AP-1/matrix metalloproteinase pathway components. J Bioenerg Biomembr 2018; 50:315-327. [PMID: 29687366 DOI: 10.1007/s10863-018-9756-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 04/05/2018] [Indexed: 10/17/2022]
Abstract
Ligustrum lucidum secoiridoid glucosides have been demonstrated to treat various types of diseases such as inflammation, pain, hepatotoxicity and hyperlipidermic as well as tonic for liver and kidney. Matrix metalloproteinases (MMPs) play a key role upon the pathology of photoaging. The present computational study showed that among the six secoiridoid glucosides (ligustroside, lucidumoside A, lucidumoside C, neonuezhenide, oleoside dimethylester, and oleuropein), ligustroside and lucidumoside A competitively inhibit all MMP-1, MMP-3, and MMP-9 activities in the docking models. The molecular docking analysis revealed a network of interactions between MMP-1, MMP-3, and MMP-9 and the ligands; ligustroside and lucidumoside A, and oxygen-containing and hydrophobic functional groups appear to be responsible for these enhanced interactions. The effect of ligustroside and lucidumoside A on the transcription factor AP-1 action was also investigated using molecular docking and dynamics simulations. The experiments suggested that inhibition of an AP-1-DNA complex formation could be on account of the direct interference of AP-1 binding onto the DNA binding sequence by ligustroside and lucidumoside A. The results suggest that both compounds have the highest potential for application as an anti-aging agent with the MMP inhibitory and anti-transcriptional activities.
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17
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Structural exploration for the refinement of anticancer matrix metalloproteinase-2 inhibitor designing approaches through robust validated multi-QSARs. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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18
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Adhikari N, Amin SA, Jha T, Gayen S. Integrating regression and classification-based QSARs with molecular docking analyses to explore the structure-antiaromatase activity relationships of letrozole-based analogs. CAN J CHEM 2017. [DOI: 10.1139/cjc-2017-0419] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aromatase is a multienzyme complex responsible for the biosynthesis of estrogen and its level has been found higher in breast cancer. Although the designing strategy of aromatase inhibitors (AIs) has continued for more than four decades, it may still be in demand to design highly effective and less toxic AIs. In this study, several chemometric approaches have been used to explore the important structural features of a series of letrozole-based analogs for their promising aromatase inhibitory activity. All techniques are statistically validated individually and in turn, validated with each other along with the structure–activity relationship (SAR) observations. The imidazole ring has been found to interact with the heme iron, whereas the triazole ring system has not shown any interaction. Moreover, imidazole function is better than 1,2,3-triazole, whereas 1,2,3-triazole is better than the 1,2,5-triazole ring system. Additionally, a bulky aryl substitution in the azole ring along with the orientation of the azole nitrogens and the cyanophenyl function has an essential role in the inhibition of aromatase. Furthermore, a cyano group substituted at the phenyl moiety interacts with Arg115, Met374, and Ser478 at the enzyme active site to form hydrogen bonding interactions. These observations are useful for designing potential AIs in the future.
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Affiliation(s)
- Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P.O. Box 17020, Jadavpur University, Kolkata 700032, (WB), India
| | - Sk. Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P.O. Box 17020, Jadavpur University, Kolkata 700032, (WB), India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P.O. Box 17020, Jadavpur University, Kolkata 700032, (WB), India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar 470003, (MP), India
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19
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Waqar M, Batool S. In silico analysis of binding interaction of conantokins with NMDA receptors for potential therapeutic use in Alzheimer's disease. J Venom Anim Toxins Incl Trop Dis 2017; 23:42. [PMID: 28943883 PMCID: PMC5607497 DOI: 10.1186/s40409-017-0132-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/13/2017] [Indexed: 01/13/2023] Open
Abstract
Background The N-methyl-D-aspartate (NMDA) receptors are glutamate receptors that play vital roles in central nervous system development and are involved in synaptic plasticity, which is an essential process for learning and memory. The subunit N-methyl D-aspartate receptor subtype 2B (NR2B) is the chief excitatory neurotransmitter receptor in the mammalian brain. Disturbances in the neurotransmission mediated by the NMDA receptor are caused by its overexposure to glutamate neurotransmitter and can be treated by its binding to an antagonist. Among several antagonists, conantokins from cone snails are reported to bind to NMDA receptors. Methods This study was designed to analyze the binding mode of conantokins with NMDA receptors in both humans and rats. To study interactions, dockings were performed using AutoDock 4.2 and their results were further analyzed using various computational tools. Results Detailed analyses revealed that these ligands can bind to active site residues of both receptors as reported in previous studies. Conclusions In light of the present results, we suggest that these conantokins can act as antagonists of those receptors and play an important role in understanding the importance of inhibition of NMDA receptors for treatment of Alzheimer’s disease.
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Affiliation(s)
- Maleeha Waqar
- Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad 45550 Pakistan
| | - Sidra Batool
- Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad 45550 Pakistan
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