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Chateau A, Van der Verren SE, Remaut H, Fioravanti A. The Bacillus anthracis Cell Envelope: Composition, Physiological Role, and Clinical Relevance. Microorganisms 2020; 8:E1864. [PMID: 33255913 PMCID: PMC7759979 DOI: 10.3390/microorganisms8121864] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/31/2022] Open
Abstract
Anthrax is a highly resilient and deadly disease caused by the spore-forming bacterial pathogen Bacillus anthracis. The bacterium presents a complex and dynamic composition of its cell envelope, which changes in response to developmental and environmental conditions and host-dependent signals. Because of their easy to access extracellular locations, B. anthracis cell envelope components represent interesting targets for the identification and development of novel therapeutic and vaccine strategies. This review will focus on the novel insights regarding the composition, physiological role, and clinical relevance of B. anthracis cell envelope components.
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Affiliation(s)
- Alice Chateau
- Avignon Université, INRAE, UMR SQPOV, F-84914 Avignon, France;
| | - Sander E. Van der Verren
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium; (S.E.V.d.V.); (H.R.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Han Remaut
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium; (S.E.V.d.V.); (H.R.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Antonella Fioravanti
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium; (S.E.V.d.V.); (H.R.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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2
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Saleem F, Mehmood R, Mehar S, Khan MTJ, Khan ZUD, Ashraf M, Ali MS, Abdullah I, Froeyen M, Mirza MU, Ahmad S. Bioassay Directed Isolation, Biological Evaluation and in Silico Studies of New Isolates from Pteris cretica L. Antioxidants (Basel) 2019; 8:E231. [PMID: 31331076 PMCID: PMC6680627 DOI: 10.3390/antiox8070231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/19/2019] [Indexed: 12/24/2022] Open
Abstract
Members of genus Pteris have their established role in the traditional herbal medicine system. In the pursuit to identify its biologically active constituents, the specie Pteris cretica L. (P. cretica) was selected for the bioassay-guided isolation. Two new maleates (F9 and CB18) were identified from the chloroform extract and the structures of the isolates were elucidated through their spectroscopic data. The putative targets, that potentially interact with both of these isolates, were identified through reverse docking by using in silico tools PharmMapper and ReverseScreen3D. On the basis of reverse docking results, both isolates were screened for their antioxidant, acetylcholinesterase (AChE) inhibition, α-glucosidase (GluE) inhibition and antibacterial activities. Both isolates depicted moderate potential for the selected activities. Furthermore, docking studies of both isolates were also studied to investigate the binding mode with respective targets followed by molecular dynamics simulations and binding free energies. Thereby, the current study embodies the poly-pharmacological potential of P. cretica.
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Affiliation(s)
- Farooq Saleem
- Punjab University College of Pharmacy, University of the Punjab, Lahore 54000, Pakistan
- Faculty of Pharmacy, University of Central Punjab, Lahore 54000, Pakistan
| | - Rashad Mehmood
- Department of Chemistry, University of Education, Vehari Campus, Vehari 61100, Pakistan
| | - Saima Mehar
- Department of Chemistry, Sardar Bahadur Khan Women University Quetta 87300, Pakistan, Pakistan
| | | | - Zaheer-Ud-Din Khan
- Botany Department, Government College University, Lahore 54000, Pakistan
| | - Muhammad Ashraf
- Department of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Muhammad Sajjad Ali
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore 54600, Pakistan
| | - Iskandar Abdullah
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium
| | - Muhammad Usman Mirza
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore 54600, Pakistan
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium
| | - Sarfraz Ahmad
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
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Ambhore AN, Kamble SS, Kadam SN, Kamble RD, Hebade MJ, Hese SV, Gaikwad MV, Meshram RJ, Gacche RN, Dawane BS. Design, synthesis and in silico study of pyridine based 1,3,4-oxadiazole embedded hydrazinecarbothioamide derivatives as potent anti-tubercular agent. Comput Biol Chem 2019; 80:54-65. [PMID: 30901601 DOI: 10.1016/j.compbiolchem.2019.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 03/05/2019] [Accepted: 03/10/2019] [Indexed: 12/15/2022]
Abstract
Development of novel, safe and effective drug candidates combating the emerging drug resistance has remained a major focus in the mainstream of anti-tuberculosis research. Here, we inspired to design and synthesize series of new pyridin-4-yl-1,3,4-oxadiazol-2-yl-thio-ethylidene-hydrazinecarbothioamide derivatives as potential anti-tubercular agents. The anti-tubercular bioactive assay demonstrated that the synthesized compounds exhibit potent anti-tubercular activity (MIC = 3.9-7.81 μg/mL) in comparison with reference drugs Rifampicin and Isoniazid.We employed pharmacophore probing approach for the identification of CYP51 as a possible drug target for the synthesized compounds. To understand the preferable binding mode, the synthesized molecules were docked onto the active site of Sterol 14 α-demethylases (CYP51) target. From the binding free energy of the docking results it was revealed that the compounds were effective CYP51 inhibitors and acts as antitubercular agent.
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Affiliation(s)
- Ajay N Ambhore
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Sonali S Kamble
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Shuddhodan N Kadam
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Rahul D Kamble
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Madhav J Hebade
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Shrikant V Hese
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Milind V Gaikwad
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Rohan J Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, MS, 411 007, India.
| | - Rajesh N Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, MS, 411 007, India.
| | - Bhaskar S Dawane
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India.
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Kuruba V, Gollapalli P. Natural radioprotectors and their impact on cancer drug discovery. Radiat Oncol J 2018; 36:265-275. [PMID: 30630265 PMCID: PMC6361248 DOI: 10.3857/roj.2018.00381] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/08/2018] [Indexed: 01/01/2023] Open
Abstract
Cancer is a complex multifaceted illness that affects different patients in discrete ways. For a number of cancers the use of chemotherapy has become standard practice. Chemotherapy is a use of cytostatic drugs to cure cancer. Cytostatic agents not only affect cancer cells but also affect the growth of normal cells; leading to side effects. Because of this, radiotherapy gained importance in treating cancer. Slaughtering of cancerous cells by radiotherapy depends on the radiosensitivity of the tumor cells. Efforts to improve the therapeutic ratio have resulted in the development of compounds that increase the radiosensitivity of tumor cells or protect the normal cells from the effects of radiation. Amifostine is the only chemical radioprotector approved by the US Food and Drug Administration (FDA), but due to its side effect and toxicity, use of this compound was also failed. Hence the use of herbal radioprotectors bearing pharmacological properties is concentrated due to their low toxicity and efficacy. Notably, in silico methods can expedite drug discovery process, to lessen the compounds with unfavorable pharmacological properties at an early stage of drug development. Hence a detailed perspective of these properties, in accordance with their prediction and measurement, are pivotal for a successful identification of radioprotectors by drug discovery process.
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Affiliation(s)
- Vinutha Kuruba
- Department of Biotechnology, NMAM Institute of Technology, Udupi, Karnataka, India
| | - Pavan Gollapalli
- Department of Biotechnology, Vignan's Foundation for Science, Technology and Research (Deemed to be University), Guntur, Andhra Pradesh, India
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Meshram RJ, Baladhye VB, Gacche RN, Karale BK, Gaikar RB. Pharmacophore Mapping Approach for Drug Target Identification: A Chemical Synthesis and in Silico Study on Novel Thiadiazole Compounds. J Clin Diagn Res 2017; 11:KF01-KF08. [PMID: 28658808 DOI: 10.7860/jcdr/2017/22761.9925] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/23/2016] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Compounds containing thiadiazole moiety are cognized to possess with variety of clinical and therapeutic activity. Finding a suitable drug target for newly synthesized compounds remain a major bottle neck in current high throughout medicinal chemistry era. AIM To effectively synthesize di substituted thiadiazole compounds and demonstrate drug target identification using an in silico pharmacophore probing approach. Moreover, we also aim to validate the suitability of identified drug target. MATERIALS AND METHODS A cost-effective and environmental friendly chemical synthesis scheme for production of di substituted thiadiazole compounds was employed. Target identification was conducted by Pharmmapper software. Validation was accomplished by performing molecular docking and further Molecular Hydrophobic Potential (MHP) analysis. RESULTS Pharmacophore probing base approach identified hepatocyte growth factor receptor (c-Met) as a suitable biological target for newly synthesized compounds. Binding free energy values indicate that compound 4b, 4e, 4g and 4h has tremendous potential to be further used as lead compound to design selective inhibitors of c-Met receptor. MHP data from current study supports the possibility that hydrophobic contacts might act as major factor stabilizing thiadiazole- c-Met complex. Moreover, in silico observations of current study are in absolute accordance with previously described in vitro and crystallographic analysis. CONCLUSION We demonstrate that thiadiazole compounds synthesized in current investigation has high potential to act in modulation of hepatocyte growth factor receptor (c-Met) activity and thereby act as putative therapeutic agent in cancer therapy.
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Affiliation(s)
- Rohan J Meshram
- Assistant Professor, The Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Vijay B Baladhye
- Assistant Professor, The Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Rajesh N Gacche
- Professor, Department of Botany, School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, Maharashtra, India
| | - Bhausaheb K Karale
- Professor, Department of Chemistry, Radhabai Kale Mahila Mahavidayalaya, Ahmednagar, Maharashtra, India
| | - Rajendra B Gaikar
- Assistant Professor, Department of Chemistry, Padmashri Vikhe Patil College, Loni, Maharashtra, India
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Secretome, surfome and immunome: emerging approaches for the discovery of new vaccine candidates against bacterial infections. World J Microbiol Biotechnol 2016; 32:155. [DOI: 10.1007/s11274-016-2107-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 06/29/2016] [Indexed: 10/21/2022]
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Identification of novel peroxisome proliferator-activated receptor-gamma (PPARγ) agonists using molecular modeling method. J Comput Aided Mol Des 2014; 28:1143-51. [PMID: 25168706 DOI: 10.1007/s10822-014-9791-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 08/23/2014] [Indexed: 10/24/2022]
Abstract
Peroxisome proliferator-activated receptor-gamma (PPARγ) plays a critical role in lipid and glucose homeostasis. It is the target of many drug discovery studies, because of its role in various disease states including diabetes and cancer. Thiazolidinediones, a synthetic class of agents that work by activation of PPARγ, have been used extensively as insulin-sensitizers for the management of type 2 diabetes. In this study, a combination of QSAR and docking methods were utilised to perform virtual screening of more than 25 million compounds in the ZINC library. The QSAR model was developed using 1,517 compounds and it identified 42,378 potential PPARγ agonists from the ZINC library, and 10,000 of these were selected for docking with PPARγ based on their diversity. Several steps were used to refine the docking results, and finally 30 potentially highly active ligands were identified. Four compounds were subsequently tested for their in vitro activity, and one compound was found to have a K i values of <5 μM.
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Tang Y, Zhu W, Chen K, Jiang H. New technologies in computer-aided drug design: Toward target identification and new chemical entity discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 3:307-13. [PMID: 24980533 PMCID: PMC7185835 DOI: 10.1016/j.ddtec.2006.09.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In the postgenomic era, computer-aided drug design (CADD) has considerably extended its range of applications, spanning almost all stages in the drug discovery pipeline, from target identification to lead discovery, from lead optimization to preclinical or clinical trials. Two new technologies of CADD associated with target identification and new chemical entity discovery will be the focus of this review. Li-he Zhang – School of Pharmaceutical Science, Peking University, Beijing, China Kaixian Chen – Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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Affiliation(s)
- Yun Tang
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weiliang Zhu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Kaixian Chen
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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Alvarez Z, Abel-Santos E. Potential use of inhibitors of bacteria spore germination in the prophylactic treatment of anthrax andClostridium difficile-associated disease. Expert Rev Anti Infect Ther 2014; 5:783-92. [PMID: 17914913 DOI: 10.1586/14787210.5.5.783] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Spore germination is the first step in establishing Bacillus and Clostridium infections. Germination is triggered by the binding of small molecules by the resting spore. Subsequently, the activated spore secretes dipicolinic acid and calcium, the spore core is rehydrated and spore structures are degraded. Inhibition of any of the germination-related events will prevent development to the vegetative stage. Inhibition of spore germination has been studied intensively in the prevention of food spoilage. In this perspective, we propose that similar approaches could be used in the prophylactic control of Bacillus anthracis and Clostridium difficile infections. Inhibition of B. anthracis spore germination could protect military and first-line emergency personnel at high risk for anthrax exposure. Inhibition of C. difficile could prevent human C. difficile-associated disease during antibiotic treatment of immunocompromised patients.
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Affiliation(s)
- Zadkiel Alvarez
- Department of Chemistry, University of Nevada, 4505 Maryland Parkway, Campus Box 4003, Las Vegas, NV 89154, USA.
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Bouzianas DG. Potential biological targets ofBacillus anthracisin anti-infective approaches against the threat of bioterrorism. Expert Rev Anti Infect Ther 2014; 5:665-84. [PMID: 17678429 DOI: 10.1586/14787210.5.4.665] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The terrorist attacks of 2001 involving anthrax underscore the imperative that safe and effective medical countermeasures should be readily available. Vaccination appears to be the most effective form of mass protection against a biological attack, but the current vaccines have drawbacks that justify the enormous amount of effort currently being put into developing more effective vaccines and other treatment modalities. After providing a comprehensive overview of the organism Bacillus anthracis as a biological weapon and its pathogenicity, this review briefly summarizes the current knowledge vital to the management of anthrax disease. This knowledge has been acquired since 2001 as a result of the progress on anthrax research and focuses on the possible development of improved human anti-infective strategies targeting B. anthracis spore components, as well as strategies based on host-pathogen interactions.
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Affiliation(s)
- Dimitrios G Bouzianas
- Department of Medical Laboratories, Faculty of Health and Care Professions, University-level Technological Educational Institute of Thessaloniki, Greece.
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Ou-Yang SS, Lu JY, Kong XQ, Liang ZJ, Luo C, Jiang H. Computational drug discovery. Acta Pharmacol Sin 2012; 33:1131-40. [PMID: 22922346 PMCID: PMC4003107 DOI: 10.1038/aps.2012.109] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 07/08/2012] [Indexed: 01/09/2023] Open
Abstract
Computational drug discovery is an effective strategy for accelerating and economizing drug discovery and development process. Because of the dramatic increase in the availability of biological macromolecule and small molecule information, the applicability of computational drug discovery has been extended and broadly applied to nearly every stage in the drug discovery and development workflow, including target identification and validation, lead discovery and optimization and preclinical tests. Over the past decades, computational drug discovery methods such as molecular docking, pharmacophore modeling and mapping, de novo design, molecular similarity calculation and sequence-based virtual screening have been greatly improved. In this review, we present an overview of these important computational methods, platforms and successful applications in this field.
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Affiliation(s)
- Si-sheng Ou-Yang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jun-yan Lu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiang-qian Kong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhong-jie Liang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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Conti P, Tamborini L, Pinto A, Blondel A, Minoprio P, Mozzarelli A, De Micheli C. Drug Discovery Targeting Amino Acid Racemases. Chem Rev 2011; 111:6919-46. [DOI: 10.1021/cr2000702] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Paola Conti
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Lucia Tamborini
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Andrea Pinto
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Arnaud Blondel
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS-URA 2185, Département de Biologie Structurale et Chimie, 25 rue du Dr. Roux, 75724 Paris, France
| | - Paola Minoprio
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosoma; Département d’Infection et Epidémiologie; 25 rue du Dr. Roux, 75724 Paris, France
| | - Andrea Mozzarelli
- Dipartimento di Biochimica e Biologia Molecolare, via G. P. Usberti 23/A, 43100 Parma, Italy
- Istituto di Biostrutture e Biosistemi, viale Medaglie d’oro, Roma, Italy
| | - Carlo De Micheli
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
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Zheng R, Chen TS, Lu T. A comparative reverse docking strategy to identify potential antineoplastic targets of tea functional components and binding mode. Int J Mol Sci 2011; 12:5200-12. [PMID: 21954353 PMCID: PMC3179160 DOI: 10.3390/ijms12085200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Revised: 07/19/2011] [Accepted: 07/22/2011] [Indexed: 12/13/2022] Open
Abstract
The main functional components of green tea, such as epigallocatechin gallate (EGCG), epigallocatechin (EGC), epicatechin gallate (ECG) and epicatechin (EC), are found to have a broad antineoplastic activity. The discovery of their targets plays an important role in revealing the antineoplastic mechanism. Therefore, to identify potential target proteins for tea polyphenols, we have taken a comparative virtual screening approach using two reverse docking systems, one based on Autodock software and the other on Tarfisdock. Two separate in silico workflows were implemented to derive a set of target proteins related to human diseases and ranked by the binding energy score. Several conventional clinically important proteins with anti-tumor effects are screened out from the PDTD protein database as the potential receptors by both procedures. To further analyze the validity of docking results, we study the binding mode of EGCG and the potential target protein Leukotriene A4 hydrolase in detail. We indicate that interactions mediated by electrostatic and hydrogen bond play a key role in ligand binding. EGCG binds to the enzyme with certain orientation and conformation that is suitable for nucleophilic attacks by several electrical residues inside the enzyme's activity cavity. This study provides useful information for studying the antitumor mechanism of tea's functional components. The comparative reverse docking strategy presented generates a tractable set of antineoplastic proteins for future experimental validation as drug targets against tumors.
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Affiliation(s)
- Rong Zheng
- Institute of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, China; E-Mail:
| | - Tuan-sheng Chen
- Institute of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; E-Mail:
| | - Tun Lu
- Institute of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, China; E-Mail:
- Fujian Supercomputer Center, Fuzhou, Fujian 350108, China
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Zhang S, Lu W, Liu X, Diao Y, Bai F, Wang L, Shan L, Huang J, Li H, Zhang W. Fast and effective identification of the bioactive compounds and their targets from medicinal plants via computational chemical biology approach. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00245c] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Testing nucleoside analogues as inhibitors of Bacillus anthracis spore germination in vitro and in macrophage cell culture. Antimicrob Agents Chemother 2010; 54:5329-36. [PMID: 20921305 DOI: 10.1128/aac.01029-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Bacillus anthracis, the etiological agent of anthrax, has a dormant stage in its life cycle known as the endospore. When conditions become favorable, spores germinate and transform into vegetative bacteria. In inhalational anthrax, the most fatal manifestation of the disease, spores enter the organism through the respiratory tract and germinate in phagosomes of alveolar macrophages. Germinated cells can then produce toxins and establish infection. Thus, germination is a crucial step for the initiation of pathogenesis. B. anthracis spore germination is activated by a wide variety of amino acids and purine nucleosides. Inosine and l-alanine are the two most potent nutrient germinants in vitro. Recent studies have shown that germination can be hindered by isomers or structural analogues of germinants. 6-Thioguanosine (6-TG), a guanosine analogue, is able to inhibit germination and prevent B. anthracis toxin-mediated necrosis in murine macrophages. In this study, we screened 46 different nucleoside analogues as activators or inhibitors of B. anthracis spore germination in vitro. These compounds were also tested for their ability to protect the macrophage cell line J774a.1 from B. anthracis cytotoxicity. Structure-activity relationship analysis of activators and inhibitors clarified the binding mechanisms of nucleosides to B. anthracis spores. In contrast, no structure-activity relationships were apparent for compounds that protected macrophages from B. anthracis-mediated killing. However, multiple inhibitors additively protected macrophages from B. anthracis.
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Liu X, Ouyang S, Yu B, Liu Y, Huang K, Gong J, Zheng S, Li Z, Li H, Jiang H. PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. Nucleic Acids Res 2010; 38:W609-14. [PMID: 20430828 PMCID: PMC2896160 DOI: 10.1093/nar/gkq300] [Citation(s) in RCA: 535] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In silico drug target identification, which includes many distinct algorithms for finding disease genes and proteins, is the first step in the drug discovery pipeline. When the 3D structures of the targets are available, the problem of target identification is usually converted to finding the best interaction mode between the potential target candidates and small molecule probes. Pharmacophore, which is the spatial arrangement of features essential for a molecule to interact with a specific target receptor, is an alternative method for achieving this goal apart from molecular docking method. PharmMapper server is a freely accessed web server designed to identify potential target candidates for the given small molecules (drugs, natural products or other newly discovered compounds with unidentified binding targets) using pharmacophore mapping approach. PharmMapper hosts a large, in-house repertoire of pharmacophore database (namely PharmTargetDB) annotated from all the targets information in TargetBank, BindingDB, DrugBank and potential drug target database, including over 7000 receptor-based pharmacophore models (covering over 1500 drug targets information). PharmMapper automatically finds the best mapping poses of the query molecule against all the pharmacophore models in PharmTargetDB and lists the top N best-fitted hits with appropriate target annotations, as well as respective molecule’s aligned poses are presented. Benefited from the highly efficient and robust triangle hashing mapping method, PharmMapper bears high throughput ability and only costs 1 h averagely to screen the whole PharmTargetDB. The protocol was successful in finding the proper targets among the top 300 pharmacophore candidates in the retrospective benchmarking test of tamoxifen. PharmMapper is available at http://59.78.96.61/pharmmapper.
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Affiliation(s)
- Xiaofeng Liu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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Klinman DM, Yamamoto M, Tross D, Tomaru K. Anthrax prevention and treatment: utility of therapy combining antibiotic plus vaccine. Expert Opin Biol Ther 2010; 9:1477-86. [PMID: 19769541 DOI: 10.1517/14712590903307347] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The intentional release of anthrax spores in 2001 confirmed this pathogen's ability to cause widespread panic, morbidity and mortality. While individuals exposed to anthrax can be successfully treated with antibiotics, pre-exposure vaccination can reduce susceptibility to infection-induced illness. Concern over the safety and immunogenicity of the licensed US vaccine (Anthrax Vaccine Adsorbed (AVA)) has fueled research into alternatives. Second-generation anthrax vaccines based on purified recombinant protective antigen (rPA) have entered clinical trials. These rPA vaccines induce neutralizing antibodies that prevent illness, but the magnitude and duration of the resultant protective response is modest. Efforts are underway to bolster the immunogenicity of rPA by combining it with adjuvants and other immunostimulatory agents. Third generation vaccines are under development that utilize a wide variety of immunization platforms, antigens, adjuvants, delivery methods and routes of delivery to optimize the induction of a protective immunity. For the foreseeable future, vaccination will rely on first and second generation vaccines co-administered with immune adjuvants. Optimal post-exposure treatment of immunologically naive individuals should include a combination of vaccine plus antibiotic therapy.
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Affiliation(s)
- Dennis M Klinman
- National Cancer Institute (NCI), NCI, NIH, Frederick, MD 21702, USA.
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18
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Couñago RM, Davlieva M, Strych U, Hill RE, Krause KL. Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames). BMC STRUCTURAL BIOLOGY 2009; 9:53. [PMID: 19695097 PMCID: PMC2743695 DOI: 10.1186/1472-6807-9-53] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 08/20/2009] [Indexed: 12/04/2022]
Abstract
BACKGROUND Bacillus anthracis is the causative agent of anthrax and a potential bioterrorism threat. Here we report the biochemical and structural characterization of B. anthracis (Ames) alanine racemase (AlrBax), an essential enzyme in prokaryotes and a target for antimicrobial drug development. We also compare the native AlrBax structure to a recently reported structure of the same enzyme obtained through reductive lysine methylation. RESULTS B. anthracis has two open reading frames encoding for putative alanine racemases. We show that only one, dal1, is able to complement a D-alanine auxotrophic strain of E. coli. Purified Dal1, which we term AlrBax, is shown to be a dimer in solution by dynamic light scattering and has a Vmax for racemization (L- to D-alanine) of 101 U/mg. The crystal structure of unmodified AlrBax is reported here to 1.95 A resolution. Despite the overall similarity of the fold to other alanine racemases, AlrBax makes use of a chloride ion to position key active site residues for catalysis, a feature not yet observed for this enzyme in other species. Crystal contacts are more extensive in the methylated structure compared to the unmethylated structure. CONCLUSION The chloride ion in AlrBax is functioning effectively as a carbamylated lysine making it an integral and unique part of this structure. Despite differences in space group and crystal form, the two AlrBax structures are very similar, supporting the case that reductive methylation is a valid rescue strategy for proteins recalcitrant to crystallization, and does not, in this case, result in artifacts in the tertiary structure.
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Affiliation(s)
- Rafael M Couñago
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Milya Davlieva
- Department of Biochemistry Rice University, Houston, TX, USA
| | - Ulrich Strych
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Ryan E Hill
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Kurt L Krause
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Mukhopadhyay S, Akmal A, Stewart AC, Hsia RC, Read TD. Identification of Bacillus anthracis spore component antigens conserved across diverse Bacillus cereus sensu lato strains. Mol Cell Proteomics 2009; 8:1174-91. [PMID: 19208616 DOI: 10.1074/mcp.m800403-mcp200] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We sought to identify proteins in the Bacillus anthracis spore, conserved in other strains of the closely related Bacillus cereus group, that elicit an immune response in mammals. Two high throughput approaches were used. First, an in silico screening identified 200 conserved putative B. anthracis spore components. A total of 192 of those candidate genes were expressed and purified in vitro, 75 of which reacted with the rabbit immune sera generated against B. anthracis spores. The second approach was to screen for cross-reacting antigens in the spore proteome of 10 diverse B. cereus group strains. Two-dimensional electrophoresis resolved more than 200 protein spots in each spore preparation. About 72% of the protein spots were found in all the strains. 18 of these conserved proteins reacted against anti-B. anthracis spore rabbit immune sera, two of which (alanine racemase, Dal-1 and the methionine transporter, MetN) overlapped the set of proteins identified using the in silico screen. A conserved repeat domain protein (Crd) was the most immunoreactive protein found broadly across B. cereus sensu lato strains. We have established an approach for finding conserved targets across a species using population genomics and proteomics. The results of these screens suggest the possibility of a multiepitope antigen for broad host range diagnostics or therapeutics against Bacillus spore infection.
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Affiliation(s)
- Sanghamitra Mukhopadhyay
- Biological Defense Research Directorate, Naval Medical Research Center, Rockville, Maryland 20852, USA
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20
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Au K, Ren J, Walter TS, Harlos K, Nettleship JE, Owens RJ, Stuart DI, Esnouf RM. Structures of an alanine racemase from Bacillus anthracis (BA0252) in the presence and absence of (R)-1-aminoethylphosphonic acid (L-Ala-P). Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:327-33. [PMID: 18453697 PMCID: PMC2376406 DOI: 10.1107/s1744309108007252] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 03/17/2008] [Indexed: 11/11/2022]
Abstract
Bacillus anthracis, the causative agent of anthrax, has been targeted by the Oxford Protein Production Facility to validate high-throughput protocols within the Structural Proteomics in Europe project. As part of this work, the structures of an alanine racemase (BA0252) in the presence and absence of the inhibitor (R)-1-aminoethylphosphonic acid (L-Ala-P) have determined by X-ray crystallography to resolutions of 2.1 and 1.47 A, respectively. Difficulties in crystallizing this protein were overcome by the use of reductive methylation. Alanine racemase has attracted much interest as a possible target for anti-anthrax drugs: not only is D-alanine a vital component of the bacterial cell wall, but recent studies also indicate that alanine racemase, which is accessible in the exosporium, plays a key role in inhibition of germination in B. anthracis. These structures confirm the binding mode of L-Ala-P but suggest an unexpected mechanism of inhibition of alanine racemase by this compound and could provide a basis for the design of improved alanine racemase inhibitors with potential as anti-anthrax therapies.
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Affiliation(s)
- Kinfai Au
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - Jingshan Ren
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - Thomas S. Walter
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - Karl Harlos
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - Joanne E. Nettleship
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - Raymond J. Owens
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - David I. Stuart
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
| | - Robert M. Esnouf
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
- Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England
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A novel immunogenic spore coat-associated protein in Bacillus anthracis: characterization via proteomics approaches and a vector-based vaccine system. Protein Expr Purif 2007; 57:72-80. [PMID: 18029197 DOI: 10.1016/j.pep.2007.08.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2007] [Revised: 08/12/2007] [Accepted: 08/20/2007] [Indexed: 12/29/2022]
Abstract
New generation anthrax vaccines have been actively explored with the aim of enhancing efficacies and decreasing undesirable side effects that could be caused by licensed vaccines. Targeting novel antigens and/or eliminating the requirements for multiple needle injections and adjuvants are major objectives in the development of new anthrax vaccines. Using proteomics approaches, we identified a spore coat-associated protein (SCAP) in Bacillus anthracis. An Escherichia coli vector-based vaccine system was used to determine the immunogenicity of SCAP. Mice generated detectable SCAP antibodies three weeks after intranasal immunization with an intact particle of ultraviolet (UV)-irradiated E. coli vector overproducing SCAP. The production of SCAP antibodies was detected via western blotting and SCAP-spotted antigen-arrays. The adjuvant effect of a UV-irradiated E. coli vector eliminates the necessity of boosting and the use of other immunomodulators which will foster the screening and manufacturing of new generation anthrax vaccines. More importantly, the immunogenic SCAP may potentially be a new candidate for the development of anthrax vaccines.
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Cai J, Han C, Hu T, Zhang J, Wu D, Wang F, Liu Y, Ding J, Chen K, Yue J, Shen X, Jiang H. Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation. Protein Sci 2006; 15:2071-81. [PMID: 16882991 PMCID: PMC2242601 DOI: 10.1110/ps.062238406] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Colonization of human stomach by the bacterium Helicobacter pylori is a major causative factor for gastrointestinal illnesses and gastric cancer. However, the discovery of anti-H. pylori agents is a difficult task due to lack of mature protein targets. Therefore, identifying new molecular targets for developing new drugs against H. pylori is obviously necessary. In this study, the in-house potential drug target database (PDTD, http://www.dddc.ac.cn/tarfisdock/) was searched by the reverse docking approach using an active natural product (compound 1) discovered by anti-H. pylori screening as a probe. Homology search revealed that, among the 15 candidates discovered by reverse docking, only diaminopimelate decarboxylase (DC) and peptide deformylase (PDF) have homologous proteins in the genome of H. pylori. Enzymatic assay demonstrated compound 1 and its derivative compound 2 are the potent inhibitors against H. pylori PDF (HpPDF) with IC50 values of 10.8 and 1.25 microM, respectively. X-ray crystal structures of HpPDF and the complexes of HpPDF with 1 and 2 were determined for the first time, indicating that these two inhibitors bind well with HpPDF binding pocket. All these results indicate that HpPDF is a potential target for screening new anti-H. pylori agents. In addition, compounds 1 and 2 were predicted to bind to HpPDF with relatively high selectivity, suggesting they can be used as leads for developing new anti-H. pylori agents. The results demonstrated that our strategy, reverse docking in conjunction with bioassay and structural biology, is effective and can be used as a complementary approach of functional genomics and chemical biology in target identification.
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Affiliation(s)
- Jianhua Cai
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Graduate School of Chinese Academy of Sciences, China
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23
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Li H, Gao Z, Kang L, Zhang H, Yang K, Yu K, Luo X, Zhu W, Chen K, Shen J, Wang X, Jiang H. TarFisDock: a web server for identifying drug targets with docking approach. Nucleic Acids Res 2006; 34:W219-24. [PMID: 16844997 PMCID: PMC1538869 DOI: 10.1093/nar/gkl114] [Citation(s) in RCA: 271] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Revised: 02/13/2006] [Accepted: 03/10/2006] [Indexed: 11/23/2022] Open
Abstract
TarFisDock is a web-based tool for automating the procedure of searching for small molecule-protein interactions over a large repertoire of protein structures. It offers PDTD (potential drug target database), a target database containing 698 protein structures covering 15 therapeutic areas and a reverse ligand-protein docking program. In contrast to conventional ligand-protein docking, reverse ligand-protein docking aims to seek potential protein targets by screening an appropriate protein database. The input file of this web server is the small molecule to be tested, in standard mol2 format; TarFisDock then searches for possible binding proteins for the given small molecule by use of a docking approach. The ligand-protein interaction energy terms of the program DOCK are adopted for ranking the proteins. To test the reliability of the TarFisDock server, we searched the PDTD for putative binding proteins for vitamin E and 4H-tamoxifen. The top 2 and 10% candidates of vitamin E binding proteins identified by TarFisDock respectively cover 30 and 50% of reported targets verified or implicated by experiments; and 30 and 50% of experimentally confirmed targets for 4H-tamoxifen appear amongst the top 2 and 5% of the TarFisDock predicted candidates, respectively. Therefore, TarFisDock may be a useful tool for target identification, mechanism study of old drugs and probes discovered from natural products. TarFisDock and PDTD are available at http://www.dddc.ac.cn/tarfisdock/.
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Affiliation(s)
- Honglin Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of SciencesShanghai 201203, China
- Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of TechnologyDalian 116023, China
| | - Zhenting Gao
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of SciencesShanghai 201203, China
| | - Ling Kang
- Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of TechnologyDalian 116023, China
| | - Hailei Zhang
- Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of TechnologyDalian 116023, China
| | - Kun Yang
- Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of TechnologyDalian 116023, China
| | - Kunqian Yu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of SciencesShanghai 201203, China
| | - Xiaomin Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of SciencesShanghai 201203, China
| | - Weiliang Zhu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of SciencesShanghai 201203, China
| | - Kaixian Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of SciencesShanghai 201203, China
| | - Jianhua Shen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of SciencesShanghai 201203, China
| | - Xicheng Wang
- Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of TechnologyDalian 116023, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of SciencesShanghai 201203, China
- School of Pharmacy, East China University of Science and TechnologyShanghai 200237, China
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