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Mahanta PJ, Lhouvum K. Plasmodium falciparum proteases as new drug targets with special focus on metalloproteases. Mol Biochem Parasitol 2024; 258:111617. [PMID: 38554736 DOI: 10.1016/j.molbiopara.2024.111617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/15/2024] [Accepted: 03/10/2024] [Indexed: 04/02/2024]
Abstract
Malaria poses a significant global health threat particularly due to the prevalence of Plasmodium falciparum infection. With the emergence of parasite resistance to existing drugs including the recently discovered artemisinin, ongoing research seeks novel therapeutic avenues within the malaria parasite. Proteases are promising drug targets due to their essential roles in parasite biology, including hemoglobin digestion, merozoite invasion, and egress. While exploring the genomic landscape of Plasmodium falciparum, it has been revealed that there are 92 predicted proteases, with only approximately 14 of them having been characterized. These proteases are further distributed among 26 families grouped into five clans: aspartic proteases, cysteine proteases, metalloproteases, serine proteases, and threonine proteases. Focus on metalloprotease class shows further role in organelle processing for mitochondria and apicoplasts suggesting the potential of metalloproteases as viable drug targets. Holistic understanding of the parasite intricate life cycle and identification of potential drug targets are essential for developing effective therapeutic strategies against malaria and mitigating its devastating global impact.
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Affiliation(s)
| | - Kimjolly Lhouvum
- Department of Biotechnology, National Institute of Technology, Arunachal Pradesh, India.
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2
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Chaurasia S, Pandey A. Molecular modelling approaches can reveal the Molecular interactions established between antimalarial targets of hemozoin pathway and the organic phytochemicals of Artocarpus species. Nat Prod Res 2024:1-9. [PMID: 38440935 DOI: 10.1080/14786419.2024.2324468] [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: 10/16/2023] [Accepted: 02/24/2024] [Indexed: 03/06/2024]
Abstract
Ayurveda, the traditional Indian medical system, has potential applications in early malaria treatment. In an in silico docking study, 50 phytochemicals from two plants Artocarpus lakoocha Roxb. (AL) And Artocarpus heterophyllus Lam. (AH), were examined for their interactions with anti-malarial proteins (PDB IDs: 3BWK, 3BPF, 1LF3). The nucleotide analogue Artemisinin, a current malaria treatment, served as a positive control. Result showed that phytochemicals from AL and AH exhibited binding affinities as high as -9.6 kcal/mol, respectively. Additionally, molecular dynamics simulation for Artocarpin: 3BPF demonstrated stable complexes over 100 ns. Notably, Artocarpin and Quercetin displayed higher binding affinities (up to -9.6 as well as -9.5 kcal/mol, respectively) compared to Artemisinin (-7.5 up to kcal/mol), have shown. Pharmacokinetic predictions indicated the compounds were likely non-carcinogenic, water-soluble and biologically safe. In-vitro analysis using β-Hematin assay supported these findings, suggesting the phytochemicals as Hemozoin pathway inhibitors.
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Affiliation(s)
- Surabhi Chaurasia
- Department of Pharmaceutical Sciences and Technology, Mesra, Jharkhand, India
| | - Anima Pandey
- Department of Pharmaceutical Sciences and Technology, Mesra, Jharkhand, India
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González JEH, Salas-Sarduy E, Alvarez LH, Valiente PA, Arni RK, Pascutti PG. Three Decades of Targeting Falcipains to Develop Antiplasmodial Agents: What have we Learned and What can be Done Next? Curr Med Chem 2024; 31:2234-2263. [PMID: 37711130 DOI: 10.2174/0929867331666230913165219] [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: 03/28/2023] [Revised: 05/06/2023] [Accepted: 07/25/2023] [Indexed: 09/16/2023]
Abstract
Malaria is a devastating infectious disease that affects large swathes of human populations across the planet's tropical regions. It is caused by parasites of the genus Plasmodium, with Plasmodium falciparum being responsible for the most lethal form of the disease. During the intraerythrocytic stage in the human hosts, malaria parasites multiply and degrade hemoglobin (Hb) using a battery of proteases, which include two cysteine proteases, falcipains 2 and 3 (FP-2 and FP-3). Due to their role as major hemoglobinases, FP-2 and FP-3 have been targeted in studies aiming to discover new antimalarials and numerous inhibitors with activity against these enzymes, and parasites in culture have been identified. Nonetheless, cross-inhibition of human cysteine cathepsins remains a serious hurdle to overcome for these compounds to be used clinically. In this article, we have reviewed key functional and structural properties of FP-2/3 and described different compound series reported as inhibitors of these proteases during decades of active research in the field. Special attention is also paid to the wide range of computer-aided drug design (CADD) techniques successfully applied to discover new active compounds. Finally, we provide guidelines that, in our understanding, will help advance the rational discovery of new FP-2/3 inhibitors.
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Affiliation(s)
- Jorge Enrique Hernández González
- Multiuser Center for Biomolecular Innovation, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
- Department of Pharmaceutical Sciences, UZA II, University of Vienna, Vienna, 1090, Austria
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo Ugalde, Universidad Nacional de San Martín, CONICET, San Martín, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnología (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina
| | | | - Pedro Alberto Valiente
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
| | | | - Pedro Geraldo Pascutti
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, RJ, Brazil
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4
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Zhang J, Wang F, Wu D, Zhao D. Revealing the mechanisms of Weishi Huogu I capsules used for treating osteonecrosis of the femoral head based on systems pharmacology with one mechanism validated with in vitro experiments. JOURNAL OF ETHNOPHARMACOLOGY 2022; 295:115354. [PMID: 35577160 DOI: 10.1016/j.jep.2022.115354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/22/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Weishi Huogu I (WH I) capsules, developed through traditional Chinese medicine, have been used to treat clinical osteonecrosis of the femoral head (ONFH) for decades. However, the mechanisms have not been systematically studied. AIM OF THE STUDY In this study, the mechanisms of WH I capsules used in treating ONFH were examined through a systems pharmacology strategy, and one mechanism was validated with in vitro experiments. MATERIALS AND METHODS WH I capsules compounds were identified by screening databases; then, a database of the potential active compounds was constructed after absorption, distribution, metabolism and excretion (ADME) evaluation. The compounds were identified through a systematic approach in which the probability of an interaction of every candidate compound with each corresponding target in the DrugBank database was calculated. Gene Ontology (GO) and pathway enrichment analyses of the targets was performed with the Metascape and KEGG DISEASE databases. Then, a compound-target network (C-T) and target-pathway network (T-P) of WH I capsule components were constructed, and network characteristics and related information were used for systematically identifying WH I capsule multicomponent-target interactions. Furthermore, the effects of WH I capsule compounds identified through the systematic pharmacology analysis of the osteogenic transformation of human umbilical mesenchymal stem cells (HUMSCs) were validated in vitro. RESULTS In total, 152 potentially important compounds and 176 associated targets were identified. Twenty-two crucial GO biological process (BP) or pathways were related to ONFH, mainly in regulatory modules regulating blood circulation, modulating growth, and affecting pathological processes closely related to ONFH. Furthermore, the GO enrichment analysis showed that corydine, isorhamnetin, and bicuculline were enriched in "RUNX2 regulates osteoblast differentiation", significantly increased alkaline phosphatase activity and calcium deposition and upregulated runt-related transcription factor 2 mRNA and protein expression and osteocalcin mRNA expression in HUMSCs, suggesting that these compounds promoted the mesenchymal stem cell (MSC) osteogenic transformation. CONCLUSIONS The study showed that the pharmacological mechanisms of WH I capsule attenuation of ONFH mainly involve three therapeutic modules: blood circulation, modulating growth, and regulating pathological processes. The crosstalk between GOBPs/pathways may constitute the basis of the synergistic effects of the compounds in WH I capsules in attenuating ONFH. One of the pharmacological mechanisms in the WH I capsule effect on ONFH involves enhancement of the osteogenic transformation of MSCs, as validated in experiments performed in vitro; however, more mechanisms should be validated in further studies.
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Affiliation(s)
- Jiaoyue Zhang
- Department of Orthopedics, Affifiliated Zhongshan Hospital of Dalian University, Dalian, 116001, China; Ansteel Group Hospital, Anshan, 114002, China.
| | - Fanli Wang
- Ansteel Group Hospital, Anshan, 114002, China.
| | - Dengbin Wu
- Ansteel Group Hospital, Anshan, 114002, China.
| | - Dewei Zhao
- Department of Orthopedics, Affifiliated Zhongshan Hospital of Dalian University, Dalian, 116001, China.
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Alberca LN, Chuguransky SR, Álvarez CL, Talevi A, Salas-Sarduy E. In silico Guided Drug Repurposing: Discovery of New Competitive and Non-competitive Inhibitors of Falcipain-2. Front Chem 2019; 7:534. [PMID: 31448257 PMCID: PMC6691349 DOI: 10.3389/fchem.2019.00534] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/12/2019] [Indexed: 11/13/2022] Open
Abstract
Malaria is among the leading causes of death worldwide. The emergence of Plasmodium falciparum resistant strains with reduced sensitivity to the first line combination therapy and suboptimal responses to insecticides used for Anopheles vector management have led to renewed interest in novel therapeutic options. Here, we report the development and validation of an ensemble of ligand-based computational models capable of identifying falcipain-2 inhibitors, and their subsequent application in the virtual screening of DrugBank and Sweetlead libraries. Among four hits submitted to enzymatic assays, two (odanacatib, an abandoned investigational treatment for osteoporosis and bone metastasis, and the antibiotic methacycline) confirmed inhibitory effects on falcipain-2, with Ki of 98.2 nM and 84.4 μM. Interestingly, Methacycline proved to be a non-competitive inhibitor (α = 1.42) of falcipain-2. The effects of both hits on falcipain-2 hemoglobinase activity and on the development of P. falciparum were also studied.
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Affiliation(s)
- Lucas N Alberca
- Laboratory of Bioactive Compounds Research and Development (LIDeB), Department of Biological Sciences, Exact Sciences College, Universidad Nacional de La Plata, La Plata, Argentina
| | - Sara R Chuguransky
- Laboratory of Bioactive Compounds Research and Development (LIDeB), Department of Biological Sciences, Exact Sciences College, Universidad Nacional de La Plata, La Plata, Argentina
| | - Cora L Álvarez
- Departamento de Biodiversidad y Biología Experimental, Facultad de Farmacia y Bioquímica, Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisico-Química Biológicas (IQUIFIB) "Prof. Alejandro C. Paladini", Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alan Talevi
- Laboratory of Bioactive Compounds Research and Development (LIDeB), Department of Biological Sciences, Exact Sciences College, Universidad Nacional de La Plata, La Plata, Argentina
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo Ugalde", Universidad Nacional de San Martín, CONICET, Buenos Aires, Argentina
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6
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Yang Y, Li Y, Zhou W, Chen Y, Wu Q, Pan Y, Zhang S, Yang L. Exploring the structural determinants of novel xanthine derivatives as A 2B adenosine receptor antagonists: a computational study. J Biomol Struct Dyn 2018; 37:3467-3481. [PMID: 30175951 DOI: 10.1080/07391102.2018.1517612] [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] [Indexed: 01/31/2023]
Abstract
Adenosine is a ubiquitous endogenous nucleoside that controls numerous physiological functions via interacting with its specific G-coupled receptors. Activation of adenosine receptors (AdoRs), particularly A2B AdoRs promotes the release of inflammatory cytokines; reduces vascular permeabilization and induces angiogenesis, thereby making A2B AdoR becomes a potentially pharmacological target for drug development. Presently, for investigating the structural determinants of 164 xanthine derivatives as A2B AdoR antagonists, we performed an in silico study integrating with 3D-QSAR, docking and molecular dynamics (MD) simulation. The obtained optimal model shows strong predictability (Q2 = 0.647, R2ncv = 0.955, and R2pred = 0.848). Additionally, to explore the binding mode of the ligand with A2B AdoR and to understand their binding mechanism, docking analysis, MD simulations (20 ns), and the calculation of binding free energy were also carried out. Finally, the structural determinants of these xanthine derivatives were identified and a total of 20 novel A2B AdoR antagonists with improved potency were computationally designed, and their synthetic feasibility and selectivity were also evaluated. The information derived from the present study offers a better appreciation for exploring the interaction mechanism of the ligand with A2B AdoR, which could be helpful for designing novel potent A2B AdoR antagonists. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yinfeng Yang
- a Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering , Dalian University of Technology , Dalian , Liaoning , China
| | - Yan Li
- a Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering , Dalian University of Technology , Dalian , Liaoning , China.,b Key Laboratory of Xinjiang Endemic Phytomedicine Resources , Pharmacy School Shihezi University, Ministry of Education , Shihezi , China
| | - Weiwei Zhou
- b Key Laboratory of Xinjiang Endemic Phytomedicine Resources , Pharmacy School Shihezi University, Ministry of Education , Shihezi , China
| | - Yaorong Chen
- a Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering , Dalian University of Technology , Dalian , Liaoning , China
| | - Qian Wu
- c Weifang , Microscale Science Institute Weifang University , Shandong , China
| | - Yanqiu Pan
- a Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering , Dalian University of Technology , Dalian , Liaoning , China
| | - Shuwei Zhang
- a Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering , Dalian University of Technology , Dalian , Liaoning , China
| | - Ling Yang
- d Laboratory of Pharmaceutical Resource Discovery , Dalian Institute of Chemical Physics , Graduate School of the Chinese Academy of Sciences , Dalian , Liaoning , China
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7
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Hernández González JE, Hernández Alvarez L, Pascutti PG, Valiente PA. Predicting binding modes of reversible peptide-based inhibitors of falcipain-2 consistent with structure-activity relationships. Proteins 2017; 85:1666-1683. [DOI: 10.1002/prot.25322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/05/2017] [Accepted: 05/17/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Jorge Enrique Hernández González
- Departamento de Física; Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho; Rua Cristóvão Colombo, 2265, Jardim Nazareth, São José do Rio Preto São Paulo CEP 15054-000 Brazil
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana; Calle 25 No. 455, entre J e I, Vedado, Plaza de la Revolución La Habana CP 10400 Cuba
| | - Lilian Hernández Alvarez
- Departamento de Física; Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho; Rua Cristóvão Colombo, 2265, Jardim Nazareth, São José do Rio Preto São Paulo CEP 15054-000 Brazil
| | - Pedro Geraldo Pascutti
- Laboratório de Dinâmica e Modelagem Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Ave. Carlos Chagas Filho, 373, CCS-Bloco D sala 30, Cidade Universitária Ilha de Fundão; Rio de Janeiro CEP 21941-902 Brazil
| | - Pedro A. Valiente
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana; Calle 25 No. 455, entre J e I, Vedado, Plaza de la Revolución La Habana CP 10400 Cuba
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8
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Amin SA, Bhargava S, Adhikari N, Gayen S, Jha T. Exploring pyrazolo[3,4-d]pyrimidine phosphodiesterase 1 (PDE1) inhibitors: a predictive approach combining comparative validated multiple molecular modelling techniques. J Biomol Struct Dyn 2017; 36:590-608. [DOI: 10.1080/07391102.2017.1288659] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sk. Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P. O. Box 17020, Kolkata 700032, West Bengal, India
| | - Sonam Bhargava
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar 470003, Madhya Pradesh, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P. O. Box 17020, Kolkata 700032, West Bengal, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar 470003, Madhya Pradesh, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P. O. Box 17020, Kolkata 700032, West Bengal, India
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9
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Binding affinity models for Falcipain inhibition based on the Linear Interaction Energy method. J Mol Graph Model 2016; 70:236-245. [DOI: 10.1016/j.jmgm.2016.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/06/2016] [Accepted: 06/15/2016] [Indexed: 02/04/2023]
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10
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Musyoka TM, Kanzi AM, Lobb KA, Bishop ÖT. Analysis of non-peptidic compounds as potential malarial inhibitors against Plasmodial cysteine proteases via integrated virtual screening workflow. J Biomol Struct Dyn 2016; 34:2084-101. [PMID: 26471975 PMCID: PMC5035544 DOI: 10.1080/07391102.2015.1108231] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
Abstract
Falcipain-2 (FP-2) and falcipain-3 (FP-3), haemoglobin-degrading enzymes in Plasmodium falciparum, are validated drug targets for the development of effective inhibitors against malaria. However, no commercial drug-targeting falcipains has been developed despite their central role in the life cycle of the parasites. In this work, in silico approaches are used to identify key structural elements that control the binding and selectivity of a diverse set of non-peptidic compounds onto FP-2, FP-3 and homologues from other Plasmodium species as well as human cathepsins. Hotspot residues and the underlying non-covalent interactions, important for the binding of ligands, are identified by interaction fingerprint analysis between the proteases and 2-cyanopyridine derivatives (best hits). It is observed that the size and chemical type of substituent groups within 2-cyanopyridine derivatives determine the strength of protein-ligand interactions. This research presents novel results that can further be exploited in the structure-based molecular-guided design of more potent antimalarial drugs.
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Affiliation(s)
- Thommas M. Musyoka
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Aquillah M. Kanzi
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Kevin A. Lobb
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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11
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Wang J, Yang Y, Li Y, Wang Y. Computational Study Exploring the Interaction Mechanism of Benzimidazole Derivatives as Potent Cattle Bovine Viral Diarrhea Virus Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:5941-5950. [PMID: 27355875 DOI: 10.1021/acs.jafc.6b01067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bovine viral diarrhea virus (BVDV) infections are prevailing in cattle populations on a worldwide scale. The BVDV RNA-dependent RNA polymerase (RdRp), as a promising target for new anti-BVDV drug development, has attracted increasing attention. To explore the interaction mechanism of 65 benzimidazole scaffold-based derivatives as BVDV inhibitors, presently, a computational study was performed based on a combination of 3D-QSAR, molecular docking, and molecular dynamics (MD) simulations. The resultant optimum CoMFA and CoMSIA models present proper reliabilities and strong predictive abilities (with Q(2) = 0. 64, R(2)ncv = 0.93, R(2)pred = 0.80 and Q(2) = 0. 65, R(2)ncv = 0.98, R(2)pred = 0.86, respectively). In addition, there was good concordance between these models, molecular docking, and MD results. Moreover, the MM-PBSA energy analysis reveals that the major driving force for ligand binding is the polar solvation contribution term. Hopefully, these models and the obtained findings could offer better understanding of the interaction mechanism of BVDV inhibitors as well as benefit the new discovery of more potent BVDV inhibitors.
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Affiliation(s)
- Jinghui Wang
- Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Pharmacy School, Ministry of Education, Shihezi University , Shihezi 832002, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology , Dalian, Liaoning 116024, P. R. China
| | - Yinfeng Yang
- Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Pharmacy School, Ministry of Education, Shihezi University , Shihezi 832002, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology , Dalian, Liaoning 116024, P. R. China
| | - Yan Li
- Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Pharmacy School, Ministry of Education, Shihezi University , Shihezi 832002, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology , Dalian, Liaoning 116024, P. R. China
| | - Yonghua Wang
- Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Pharmacy School, Ministry of Education, Shihezi University , Shihezi 832002, China
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12
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Yang Y, Li Y, Pan Y, Wang J, Lin F, Wang C, Zhang S, Yang L. Computational Analysis of Structure-Based Interactions for Novel H₁-Antihistamines. Int J Mol Sci 2016; 17:ijms17010129. [PMID: 26797608 PMCID: PMC4730370 DOI: 10.3390/ijms17010129] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/05/2016] [Accepted: 01/13/2016] [Indexed: 12/31/2022] Open
Abstract
As a chronic disorder, insomnia affects approximately 10% of the population at some time during their lives, and its treatment is often challenging. Since the antagonists of the H₁ receptor, a protein prevalent in human central nervous system, have been proven as effective therapeutic agents for treating insomnia, the H₁ receptor is quite possibly a promising target for developing potent anti-insomnia drugs. For the purpose of understanding the structural actors affecting the antagonism potency, presently a theoretical research of molecular interactions between 129 molecules and the H₁ receptor is performed through three-dimensional quantitative structure-activity relationship (3D-QSAR) techniques. The ligand-based comparative molecular similarity indices analysis (CoMSIA) model (Q² = 0.525, R²ncv = 0.891, R²pred = 0.807) has good quality for predicting the bioactivities of new chemicals. The cross-validated result suggests that the developed models have excellent internal and external predictability and consistency. The obtained contour maps were appraised for affinity trends for the investigated compounds, which provides significantly useful information in the rational drug design of novel anti-insomnia agents. Molecular docking was also performed to investigate the mode of interaction between the ligand and the active site of the receptor. Furthermore, as a supplementary tool to study the docking conformation of the antagonists in the H₁ receptor binding pocket, molecular dynamics simulation was also applied, providing insights into the changes in the structure. All of the models and the derived information would, we hope, be of help for developing novel potent histamine H₁ receptor antagonists, as well as exploring the H₁-antihistamines interaction mechanism.
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Affiliation(s)
- Yinfeng Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Yan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Yanqiu Pan
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Jinghui Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Feng Lin
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Chao Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Shuwei Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Ling Yang
- Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics, Graduate School of the Chinese Academy of Sciences, Dalian 116023, China.
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Li Y, Wang J, Xiao Y, Wang Y, Chen S, Yang Y, Lu A, Zhang S. A systems pharmacology approach to investigate the mechanisms of action of Semen Strychni and Tripterygium wilfordii Hook F for treatment of rheumatoid arthritis. JOURNAL OF ETHNOPHARMACOLOGY 2015; 175:301-314. [PMID: 26386382 DOI: 10.1016/j.jep.2015.09.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/02/2015] [Accepted: 09/13/2015] [Indexed: 06/05/2023]
Abstract
ETHNOPHARMACOLOGY RELEVANCE The angiogenesis control at the initiation of rheumatoid arthritis (RA) that mainly blocks the inflammatory cascades expects to attenuate the action of angiogenic mediators, synovial angiogenesis, and to partially reverse the erosive bone damage. Two typical Chinese herbs, Semen Strychni and Tripterygium wilfordii Hook F (TwHF) have been used as a remedy to treat RA since ancient time. However, their functioning mechanisms are still unknown. Thus it is necessary to exploit their underlying mechanism for the treatment of RA. METHODS This study was undertaken to analyze their underlying mechanism based on a systems biology platform. Firstly, active components of the two herbs were screened out from TcmSP database based on their OB and DL values. Then their potential targets were predicted by using Random Forest, Support Vector Machine, and validated via docking process. Finally, a network of compound-target was constructed. RESULTS In this work, 27 and 33 active compounds were screened out from Semen Strychni and TwHF, targeting 28 and 32 potential proteins, respectively. The results show that the two herbs modulate the angiogenesis mediators through both direct and indirect pathways, and 21 common targets shared by Semen Strychni and TwHF bear major responsibility for treating RA. CONCLUSIONS The underlying mechanism of Semen Strychni and TwHF in treatment of RA is through multiple targets interaction by their blocking of the angiogenesis mediator cascades. This may provide us a better understanding of the function of the two herbs for the treatment of RA, as well as a clue to unveil their possible treatment effects of other systemic diseases, and in this way, hopefully the screening models may facilitate the discovery of novel combined drugs.
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Affiliation(s)
- Yan Li
- Key laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, PR China.
| | - Jinghui Wang
- Key laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, PR China
| | - Yuanchun Xiao
- Key laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, PR China
| | - Yonghua Wang
- Center of Bioinformatics, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Sushing Chen
- Department of Computer Information Science & Engineering, Systems Biology Lab, University of Florida-Gainesville, FL 32611, USA
| | - Yinfeng Yang
- Key laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, PR China
| | - Aiping Lu
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong 999077, Hong Kong
| | - Shuwei Zhang
- Key laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, PR China
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Insights into activity enhancement of 4-aminoquinoline-based hybrids using atom-based and field-based QSAR studies. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1195-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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