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Patoliya J, Thaker K, Rabadiya K, Patel D, Jain NK, Joshi R. Uncovering the Interaction Interface Between Harpin (Hpa1) and Rice Aquaporin (OsPIP1;3) Through Protein-Protein Docking: An In Silico Approach. Mol Biotechnol 2024; 66:756-768. [PMID: 36807270 DOI: 10.1007/s12033-023-00690-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/07/2023] [Indexed: 02/23/2023]
Abstract
Hpa1 (a type of harpin) is involved in T3SS (Type III Secretion System) assembly in the infection mechanism by Xanthomonas Oryzae pv. oryzae (Xoo). Hpa1 interacts with the plasma membrane components of plants thereby assisting effector proteins toward the cytoplasm, wherein effectors execute their pathological functions. Independently, harpins also induce hypersensitive response and systemic acquired resistance in plants. However, lack of knowledge regarding the plant-harpin interaction mechanism constrains the pathway of its agricultural application. Although an in vitro study proved that Hpa1 protein can interact with OsPIP1;3, a rice aquaporin, the structural basis of the interaction is yet to be discovered. The presented work is the first of its kind where an in silico approach is used for the PPI (protein-protein interaction) of harpin protein. The study discovered participation of Hpa1 N-terminal amino acids at the interface. Besides, MD simulation studies were performed to assess the stability. RMSD values were 0.35 ± 0.049, 0.73 ± 0.11, and 0.50 ± 0.065 nm for OsPIP1;3, Hpa1, and Hpa1-OsPIP1;3 complex, respectively. Additionally, Residue-wise fluctuations have also been studied post-MDS. Taken together, these findings not only give a solid foundation for a deeper knowledge of various interacting target molecules with Harpin protein orthologs but also bring a new avenue for the structural-functional relationship study of harpin proteins.
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Affiliation(s)
- Jaimini Patoliya
- Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Khushali Thaker
- Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Khushbu Rabadiya
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Dhaval Patel
- Gujarat Biotechnology University, Gandhinagar, Gujarat, 382355, India
| | - Nayan K Jain
- Department of Life Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Rushikesh Joshi
- Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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Kumar C, P.T.V. L, Arunachalam A. Structure based pharmacophore study to identify possible natural selective PARP-1 trapper as anti-cancer agent. Comput Biol Chem 2019; 80:314-323. [DOI: 10.1016/j.compbiolchem.2019.04.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 02/06/2023]
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Beck KR, Kaserer T, Schuster D, Odermatt A. Virtual screening applications in short-chain dehydrogenase/reductase research. J Steroid Biochem Mol Biol 2017; 171:157-177. [PMID: 28286207 PMCID: PMC6831487 DOI: 10.1016/j.jsbmb.2017.03.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 03/06/2017] [Accepted: 03/08/2017] [Indexed: 02/06/2023]
Abstract
Several members of the short-chain dehydrogenase/reductase (SDR) enzyme family play fundamental roles in adrenal and gonadal steroidogenesis as well as in the metabolism of steroids, oxysterols, bile acids, and retinoids in peripheral tissues, thereby controlling the local activation of their cognate receptors. Some of these SDRs are considered as promising therapeutic targets, for example to treat estrogen-/androgen-dependent and corticosteroid-related diseases, whereas others are considered as anti-targets as their inhibition may lead to disturbances of endocrine functions, thereby contributing to the development and progression of diseases. Nevertheless, the physiological functions of about half of all SDR members are still unknown. In this respect, in silico tools are highly valuable in drug discovery for lead molecule identification, in toxicology screenings to facilitate the identification of hazardous chemicals, and in fundamental research for substrate identification and enzyme characterization. Regarding SDRs, computational methods have been employed for a variety of applications including drug discovery, enzyme characterization and substrate identification, as well as identification of potential endocrine disrupting chemicals (EDC). This review provides an overview of the efforts undertaken in the field of virtual screening supported identification of bioactive molecules in SDR research. In addition, it presents an outlook and addresses the opportunities and limitations of computational modeling and in vitro validation methods.
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Affiliation(s)
- Katharina R Beck
- Swiss Center for Applied Human Toxicology and Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), Computer Aided Molecular Design Group, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Daniela Schuster
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), Computer Aided Molecular Design Group, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
| | - Alex Odermatt
- Swiss Center for Applied Human Toxicology and Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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Mahesh R, Nayak VL, Babu KS, Riyaz S, Shaik TB, Kumar GB, Mallipeddi PL, Reddy CR, Shekar KC, Jose J, Nagesh N, Kamal A. Design, Synthesis, and in vitro and in vivo Evaluations of (Z)-3,4,5-Trimethoxystyrylbenzenesulfonamides/sulfonates as Highly Potent Tubulin Polymerization Inhibitors. ChemMedChem 2017; 12:678-700. [PMID: 28276645 DOI: 10.1002/cmdc.201600643] [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: 12/26/2016] [Revised: 03/04/2017] [Indexed: 01/11/2023]
Abstract
Newer therapeutics can be developed in drug discovery by adopting the strategy of scaffold hopping of the privileged scaffolds from known bioactive compounds. This strategy has been widely employed in drug-discovery processes. Structure-based docking studies illustrate the basic underlying concepts and reveal that interactions of the sulfonamide group and hydrophobic interactions are crucial. On the basis of this strategy, over 60 synthetic analogues were synthesized and evaluated for their cytotoxicity against the NCI panel of 60 human cancer cell lines; the majority of these compounds exhibited promising cytotoxicity with GI50 values ranging between 18 and 50 nm. Among these compounds, (Z)-N-[2,3-dimethoxy-5-(3,4,5-trimethoxystyryl)phenyl]-4-methoxybenzenesulfonamide (7 a) and (Z)-N-[2-hydroxy-3-methoxy-6-(3,4,5-trimethoxystyryl)phenyl]-4-methoxybenzenesulfonamide (9 a) were found to be potent. Similar results were obtained against three human cancer cell lines with IC50 values ranging between 0.04 and 3.0 μm. Studies aimed at elucidating the mechanism of action of these new analogues revealed that they inhibited the in vitro polymerization of tubulin and disorganized the assembly of microtubules in HeLa and MCF-7cancer cells. Lead compounds 7 a and 9 a displayed notable in vivo antitumor activity in a HeLa tumor xenograft model. Our studies have resulted in the identification of a scaffold that can target tubulin polymerization, which should have significant potential toward the development of new antitumor drugs.
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Affiliation(s)
- Rasala Mahesh
- Medicinal Chemistry and Pharmacology Division, CSIR-IICT, Uppal Road, Hyderabad, 500007, India
| | - Vadithe Lakshma Nayak
- Medicinal Chemistry and Pharmacology Division, CSIR-IICT, Uppal Road, Hyderabad, 500007, India
| | - Korrapati Suresh Babu
- Medicinal Chemistry and Pharmacology Division, CSIR-IICT, Uppal Road, Hyderabad, 500007, India
| | - Syed Riyaz
- Medicinal Chemistry and Pharmacology Division, CSIR-IICT, Uppal Road, Hyderabad, 500007, India
| | - Thokhir Basha Shaik
- Medicinal Chemistry and Pharmacology Division, CSIR-IICT, Uppal Road, Hyderabad, 500007, India
| | - Gajjela Bharth Kumar
- Medicinal Chemistry and Pharmacology Division, CSIR-IICT, Uppal Road, Hyderabad, 500007, India
| | | | - Challa Ratna Reddy
- Medicinal Chemistry and Pharmacology Division, CSIR-IICT, Uppal Road, Hyderabad, 500007, India
| | - Kunta Chandra Shekar
- Medicinal Chemistry and Pharmacology Division, CSIR-IICT, Uppal Road, Hyderabad, 500007, India
| | - Jedy Jose
- CSIR-CCMB, Uppal Road, Hyderabad, 500007, India
| | | | - Ahmed Kamal
- Medicinal Chemistry and Pharmacology Division, CSIR-IICT, Uppal Road, Hyderabad, 500007, India.,Department of Medicinal Chemistry, NIPER-Hyderabad, 40, Dilip Road, Hyderabad, 500037, India
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Predicting potential antitumor targets of Aconitum alkaloids by molecular docking and protein–ligand interaction fingerprint. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1553-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kaalia R, Kumar A, Srinivasan A, Ghosh I. An Ab Initio Method for Designing Multi-Target Specific Pharmacophores using Complementary Interaction Field of Aspartic Proteases. Mol Inform 2015; 34:380-93. [PMID: 27490384 DOI: 10.1002/minf.201400157] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/09/2014] [Indexed: 11/09/2022]
Abstract
For past few decades, key objectives of rational drug discovery have been the designing of specific and selective ligands for target proteins. Infectious diseases like malaria are continuously becoming resistant to traditional medicines, which inculcates need for new approaches to design inhibitors for antimalarial targets. A novel method for ab initio designing of multi target specific pharmacophores using the interaction field maps of active sites of multiple proteins has been developed to design 'specificity' pharmacophores for aspartic proteases. The molecular interaction field grid maps of active sites of aspartic proteases (plasmepsin II & IV from Plasmodium falciparum, plasmepsin from Plasmodium vivax, pepsin & cathepsin D from human) are calculated and common pharmacophoric features for favourable binding spots in active sites are extracted in the form of cliques of graphs using inductive logic programming (ILP). The two pharmacophore ensembles are constructed from largest common cliques by imposing size of receptor active site (L) and domain-specific receptor-ligand information (S). The overlap of chemical space between two ensembles and the results of virtual screening of inhibitor database with known activities show that this method can design efficient pharmacophores with no prior ligand information.
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Affiliation(s)
- Rama Kaalia
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India phone/fax:9971287771
| | - Amit Kumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India phone/fax:9971287771
| | - Ashwin Srinivasan
- Indraprastha Institute of Information Technology, New Delhi-110020, India.,Current address: Department of Computer Science, BITS-Pilani, Goa-403726, India
| | - Indira Ghosh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India phone/fax:9971287771.
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Serrano M, Kombrink E, Meesters C. Considerations for designing chemical screening strategies in plant biology. FRONTIERS IN PLANT SCIENCE 2015; 6:131. [PMID: 25904921 PMCID: PMC4389374 DOI: 10.3389/fpls.2015.00131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/18/2015] [Indexed: 05/03/2023]
Abstract
Traditionally, biologists regularly used classical genetic approaches to characterize and dissect plant processes. However, this strategy is often impaired by redundancy, lethality or pleiotropy of gene functions, which prevent the isolation of viable mutants. The chemical genetic approach has been recognized as an alternative experimental strategy, which has the potential to circumvent these problems. It relies on the capacity of small molecules to modify biological processes by specific binding to protein target(s), thereby conditionally modifying protein function(s), which phenotypically resemble mutation(s) of the encoding gene(s). A successful chemical screening campaign comprises three equally important elements: (1) a reliable, robust, and quantitative bioassay, which allows to distinguish between potent and less potent compounds, (2) a rigorous validation process for candidate compounds to establish their selectivity, and (3) an experimental strategy for elucidating a compound's mode of action and molecular target. In this review we will discuss details of this general strategy and additional aspects that deserve consideration in order to take full advantage of the power provided by the chemical approach to plant biology. In addition, we will highlight some success stories of recent chemical screenings in plant systems, which may serve as teaching examples for the implementation of future chemical biology projects.
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Affiliation(s)
- Mario Serrano
- Plant Biology, Department of Biology, University of FribourgFribourg, Switzerland
| | - Erich Kombrink
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding ResearchKöln, Germany
| | - Christian Meesters
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding ResearchKöln, Germany
- Department of Chemical Biology, Faculty of Biology, Center for Medical Biotechnology, University of Duisburg-EssenEssen, Germany
- *Correspondence: Christian Meesters, Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Köln, Germany
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He L, Dai R, Zhang XR, Gao SY, He YY, Wang LB, Gao X, Yang LQ. Ligand-based 3D pharmacophore design, virtual screening and molecular docking for novel p38 MAPK inhibitors. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1158-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Randhawa V, Sharma P, Bhushan S, Bagler G. Identification of key nodes of type 2 diabetes mellitus protein interactome and study of their interactions with phloridzin. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:302-17. [PMID: 23692363 DOI: 10.1089/omi.2012.0115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Network biology-inspired approaches could be used effectively in probing regulatory processes by which small molecules intervene with disease mechanisms. The present study aims at identification of key targets of type 2 diabetes mellitus (T2DM) by network analysis of the underlying protein interactome, and probing for mechanisms by which phloridzin could be critical at altering the disease phenotype. Towards this goal, we constructed a protein-protein interaction network associated with T2DM, starting from candidate genes and systems-level interactions data available. The relevance of the network constructed was verified with the help of gene ontology, node deletion, and biological essentiality studies. Using a network analysis method, MAPK1, EP300, and SMAD2 were identified as the most central proteins of potential therapeutic value. Phloridzin, a known antidiabetic agent, potentially interacts with proteins central to T2DM mechanisms. The structural understanding of interaction of phloridzin with these proteins of relevance to T2DM could provide better insight into its regulatory mechanisms and help in developing better therapeutic agents. The molecular docking results suggest that phloridzin is potentially involved in making critical interactions with MAPK1. These results could further be validated by experimental studies and could be used to design therapeutic agents for T2DM intervention.
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Affiliation(s)
- Vinay Randhawa
- Biotechnology Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research (CSIR-IHBT), Palampur, India
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