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"protein docking"

S S Bhunia, A K Saxena
The GPVI receptor on the platelets plays a major role in inhibiting arterial thrombosis with limited risk of bleeding and is considered a potential anti-thrombotic target for arterial thrombosis. In the reported anti-thrombotics, tetrahydropyridoindoles, the title compound was the best inhibitor of the collagen mediated platelet aggregation by antagonizing the platelet receptor GPVI. Interestingly, the racemic title compound showed better antagonism (IC50 racemate = 6.7 μM) than either of its enantiomers (IC50 S enantiomer = 25...
November 14, 2017: SAR and QSAR in Environmental Research
Natalia Platonova, Chiara Parravicini, Cristina Sensi, Alessandro Paoli, Michela Colombo, Antonino Neri, Ivano Eberini, Raffaella Chiaramonte
Notch signaling plays an important role in several cellular functions including growth, differentiation, cell fate determination and stemness. Increased Notch activity has been linked to several types of cancers. Activation of Notch signaling is triggered by the interaction of Notch receptors (Notch1-4) with 5 different ligands (Jagged1-2 and Dll1-3-4) expressed on the neighbouring cells. Currently, indirect approaches to inhibit Notch signalling are based on the inhibition of the key step of Notch activation catalyzed by the γ-Secretase and thereby affect several different γ-Secretase substrates; conversely direct strategies get advantage of antibody-based drugs...
2017: PloS One
Betty Daneial, Jacob Paul Vazhappilly Joseph, Guruprasad Ramakrishna
Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been associated in a series of cellular processes like cell migration and survival. FAK inhibition by an anti cancer agent is critical. Therefore, it is of interest to identify, modify, design, improve and develop molecules to inhibit FAK. Solanesol is known to have inhibitory activity towards FAK. However, the molecular principles of its binding with FAK is unknown. Solanesol is a highly flexible ligand (25 rotatable bonds)...
2017: Bioinformation
Manuel Alejandro Marín-López, Joan Planas-Iglesias, Joaquim Aguirre-Plans, Jaume Bonet, Javier Garcia-Garcia, Narcis Fernandez-Fuentes, Baldo Oliva
Motivation: The characterization of the protein-protein association mechanisms is crucial to understanding how biological processes occur. It has been previously shown that the early formation of non-specific encounters enhances the realization of the stereospecific (i.e. native) complex by reducing the dimensionality of the search process. The association rate for the formation of such complex plays a crucial role in the cell biology and depends on how the partners diffuse to be close to each other...
September 27, 2017: Bioinformatics
Francesca Nadalin, Alessandra Carbone
Motivation: Large-scale computational docking will be increasingly used in future years to discriminate protein-protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein-protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations. Results: We propose CIPS (Combined Interface Propensity for decoy Scoring), a new pair potential combining interface composition with residue-residue contact preference...
September 22, 2017: Bioinformatics
Horia Jalily Hasani, Marawan Ahmed, Khaled Barakat
The voltage-gated KCNQ1/KCNE1 potassium ion channel complex, forms the slow delayed rectifier (IKs) current in the heart, which plays an important role in heart signaling. The importance of KCNQ1/KCNE1 channel's function is further implicated by the linkage between loss-of-function and gain-of-function mutations in KCNQ1 or KCNE1, and long QT syndromes, congenital atrial fibrillation, and short QT syndrome. Also, KCNQ1/KCNE1 channels are an off-target for many non-cardiovascular drugs, leading to fatal cardiac irregularities...
September 29, 2017: Journal of Molecular Graphics & Modelling
Hervé Hogues, Traian Sulea, Francis Gaudreault, Christopher R Corbeil, Enrico O Purisima
The Farnesoid X receptor (FXR) exhibits significant backbone movement in response to the binding of various ligands and can be a challenge for pose prediction algorithms. As part of the D3R Grand Challenge 2, we tested Wilma-SIE, a rigid-protein docking method, on a set of 36 FXR ligands for which the crystal structures had originally been blinded. These ligands covered several classes of compounds. To overcome the rigid protein limitations of the method, we used an ensemble of publicly available structures for FXR from the PDB...
October 5, 2017: Journal of Computer-aided Molecular Design
Mansi Aggarwal, Aditi Singh, Sonam Grover, Bharati Pandey, Anchala Kumari, Abhinav Grover
Mycobacterium tuberculosis (Mtb) resistance towards anti-tuberculosis drugs is a widespread problem. Pyrazinamide (PZA) is a first line antitubercular drug that kills semi-dormant bacilli when converted into its activated form i.e. pyrazinoic acid (POA) by Pyrazinamidase (PZase) enzyme coded by pncA gene. In this study, we conducted several analyses on native and mutant structures (W68R, W68G) of PZase before and after docking with the PZA drug to explore the molecular mechanism behind PZA resistance caused due to pncA mutations...
October 5, 2017: Journal of Cellular Biochemistry
Sameeksha Tiwari, Manika Awasthi, Swati Singh, Veda P Pandey, Upendra N Dwivedi
Protein-protein interactions (PPI) are a new emerging class of novel therapeutic targets. In order to probe these interactions, computational tools provide a convenient and quick method towards the development of therapeutics. Keeping this in view the present study was initiated to analyze interaction of tumour suppressor protein p53 (TP53) and breast cancer associated protein (BRCA1) as promising target against breast cancer. Using computational approaches such as protein-protein docking, hot spot analyses, molecular docking and molecular dynamics simulation (MDS), stepwise analyses of the interactions of the wild type and mutant TP53 with that of wild type BRCA1 and their modulation by alkaloids were done...
October 5, 2017: Journal of Biomolecular Structure & Dynamics
Brian Jiménez-García, Jorge Roel-Touris, Miguel Romero-Durana, Miquel Vidal, Daniel Jiménez-González, Juan Fernández-Recio
Motivation: Computational prediction of protein-protein complex structure by docking can provide structural and mechanistic insights for protein interactions of biomedical interest. However, current methods struggle with difficult cases, such as those involving flexible proteins, low-affinity complexes or transient interactions. A major challenge is how to efficiently sample the structural and energetic landscape of the association at different resolution levels, given that each scoring function is often highly coupled to a specific type of search method...
September 4, 2017: Bioinformatics
Matteo T Degiacomi, Carla Schmidt, Andrew J Baldwin, Justin L P Benesch
Chemical crosslinking can identify the neighborhood relationships between specific amino-acid residues in proteins. The interpretation of crosslinking data is typically performed using single, static atomic structures. However, proteins are dynamic, undergoing motions spanning from local fluctuations of individual residues to global motions of protein assemblies. Here we demonstrate that failure to explicitly accommodate dynamics when interpreting crosslinks structurally can lead to considerable errors. We present a method and associated software, DynamXL, which is able to account directly for flexibility in the context of crosslinking modeling...
November 7, 2017: Structure
Taek-In Oh, Yoon-Mi Lee, Taek-Jin Nam, Young-San Ko, Shinmee Mah, Jinhee Kim, Younghoon Kim, Rallabandi Harikrishna Reddy, Young Jun Kim, Sungwoo Hong, Ji-Hong Lim
Fascaplysin has been reported to exert anti-cancer effects by inhibiting cyclin-dependent kinase 4 (CDK4); however, the precise mode of action by which fascaplysin suppresses tumor growth is not clear. Here, we found that fascaplysin has stronger anti-cancer effects than other CDK4 inhibitors, including PD0332991 and LY2835219, on lung cancer cells that are wild-type or null for retinoblastoma (RB), indicating that unknown target molecules might be involved in the inhibition of tumor growth by fascaplysin. Fascaplysin treatment significantly decreased tumor angiogenesis and increased cleaved-caspase-3 in xenografted tumor tissues...
September 29, 2017: International Journal of Molecular Sciences
Tanay Kumar Saha, Ataur Katebi, Wajdi Dhifli, Mohammad Al Hasan
Modeling the interface region of a protein complex paves the way for understanding its dynamics and functionalities. Existing works model the interface region of a complex by using different approaches, such as, the residue composition at the interface region, the geometry of the interface residues, or the structural alignment of interface regions. These approaches are useful for ranking a set of docked conformation or for building scoring function for protein-protein docking, but they do not provide a generic and scalable technique for the extraction of interface patterns leading to functional motif discovery...
September 26, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Rocco Moretti, Sergey Lyskov, Rhiju Das, Jens Meiler, Jeffrey J Gray
The Rosetta molecular modeling software package provides a large number of experimentally validated tools for modeling and designing proteins, nucleic acids, and other biopolymers, with new protocols being added continually. While freely available to academic users, external usage is limited by the need for expertise in the Unix command line environment. To make Rosetta protocols available to a wider audience, we previously created a web server called Rosetta Online Server that Includes Everyone (ROSIE), which provides a common environment for hosting web-accessible Rosetta protocols...
September 28, 2017: Protein Science: a Publication of the Protein Society
Tamjeed Saleh, Paolo Rossi, Charalampos G Kalodimos
The activity of protein kinases is often regulated in an intramolecular fashion by signaling domains, which feature several phosphorylation or protein-docking sites. How kinases integrate such distinct binding and signaling events to regulate their activities is unclear, especially in quantitative terms. We used NMR spectroscopy to show how structural elements within the Abl regulatory module (RM) synergistically generate a multilayered allosteric mechanism that enables Abl kinase to function as a finely tuned switch...
November 2017: Nature Structural & Molecular Biology
Faheem Ahmed Khan, Hui Liu, Hao Zhou, Kai Wang, Muhammad Tahir Ul Qamar, Nuruliarizki Shinta Pandupuspitasari, Zhang Shujun
The biology of sperm, its capability of fertilizing an egg and its role in sex ratio are the major biological questions in reproductive biology. To answer these question we integrated X and Y chromosome transcriptome across different species: Bos taurus and Sus scrofa and identified reproductive driver genes based on Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm. Our strategy resulted in 11007 and 10445 unique genes consisting of 9 and 11 reproductive modules in Bos taurus and Sus scrofa, respectively...
August 15, 2017: Oncotarget
Petras J Kundrotas, Ivan Anishchenko, Taras Dauzhenka, Ian Kotthoff, Daniil Mnevets, Matthew M Copeland, Ilya A Vakser
Characterization of life processes at the molecular level requires structural details of protein interactions. The number of experimentally determined structures of protein-protein complexes accounts only for a fraction of known protein interactions. This gap in structural description of the interactome has to be bridged by modeling. An essential part of the development of structural modeling/docking techniques for protein interactions is databases of protein-protein complexes. They are necessary for studying protein interfaces, providing a knowledge base for docking algorithms, developing intermolecular potentials, search procedures, and scoring functions...
September 10, 2017: Protein Science: a Publication of the Protein Society
Amit Rahi, Alisha Dhiman, Damini Singh, Andrew M Lynn, Mohd Rehan, Rakesh Bhatnagar
Surface localized microbial enolases' binding with human plasminogen has been increasingly proven to have an important role in initial infection cycle of several human pathogens.Likewise, surface localized Mycobacterium tuberculosis (Mtb) enolase also binds to human plasminogen, and this interaction may entail crucial consequences for granuloma stability. The current study is the first attempt to explore the plasminogen interacting residues of enolase from Mtb. Beginning with the structural modeling of Mtbenolase, the binding pose of Mtbenolase and human plasminogen was predicted using protein-protein docking simulations...
September 9, 2017: Journal of Cellular Biochemistry
Michael Estrin, Haim J Wolfson
Motivation: A highly efficient template-based protein-protein docking algorithm, nicknamed SnapDock, is presented. It employs a Geometric Hashing-based structural alignment scheme to align the target proteins to the interfaces of non-redundant protein-protein interface libraries. Docking of a pair of proteins utilizing the 22 600 interface PIFACE library is performed in < 2 min on the average. A flexible version of the algorithm allowing hinge motion in one of the proteins is presented as well...
July 15, 2017: Bioinformatics
Kimia Hirbod, Leili Jalili-Baleh, Hamid Nadri, Seyed Esmaeil Sadat Ebrahimi, Alireza Moradi, Bahar Pakseresht, Alireza Foroumadi, Abbas Shafiee, Mehdi Khoobi
OBJECTIVES: To investigate the efficiency of a novel series of coumarin derivatives bearing benzoheterocycle moiety as novel cholinesterase inhibitors. MATERIALS AND METHODS: Different 7-hydroxycoumarin derivatives were synthesized via Pechmann or Knoevenagel condensation and conjugated to different benzoheterocycle (8-hydroxyquinoline, 2-mercaptobenzoxazole or 2-mercaptobenzimidazole) using dibromoalkanes 3a-m: Final compounds were evaluated against acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) by Ellman's method...
June 2017: Iranian Journal of Basic Medical Sciences
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