Prospects of multitarget drug designing strategies by linking molecular docking and molecular dynamics to explore the protein-ligand recognition process

scientific article published on 23 April 2020

Prospects of multitarget drug designing strategies by linking molecular docking and molecular dynamics to explore the protein-ligand recognition process is …
instance of (P31):
review articleQ7318358
scholarly articleQ13442814

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P356DOI10.1002/DDR.21673
P698PubMed publication ID32329098

P50authorC. Benjamin NamanQ85961322
T P SajeevanQ90444924
Krishnankutty Chandrika SivakumarQ93202750
P2093author name stringJin Haixiao
P2860cites workCHARMM: the biomolecular simulation programQ24658108
Computational methods in drug discoveryQ26997089
Established and emerging trends in computational drug discovery in the structural genomics eraQ27011910
Shifting from the single to the multitarget paradigm in drug discoveryQ27144242
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databasesQ27231136
Altered brain energetics induces mitochondrial fission arrest in Alzheimer's DiseaseQ27302961
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreadingQ27860652
Modelling protein docking using shape complementarity, electrostatics and biochemical informationQ28249132
eHiTS: a new fast, exhaustive flexible ligand docking systemQ28253448
Prospect of a dopamine contribution in the next generation of antidepressant drugs: the triple reuptake inhibitorsQ28256136
Computer-aided drug design: the next 20 yearsQ28256647
Efficacy and safety of sunitinib in patients with advanced gastrointestinal stromal tumour after failure of imatinib: a randomised controlled trialQ28268831
Sunitinib versus interferon alfa in metastatic renal-cell carcinomaQ28282757
Multi-target drugs: the trend of drug research and developmentQ28480888
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94Q28842789
ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformationQ29010774
Development and testing of a general amber force fieldQ29547642
A semiempirical free energy force field with charge-based desolvationQ29614316
Dynamic personalities of proteinsQ29616723
Empirical scoring functions for advanced protein-ligand docking with PLANTS.Q51857293
Validation studies of the site-directed docking program LibDock.Q51901678
Knowledge-based scoring function to predict protein-ligand interactions.Q52083236
Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins.Q52132563
Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites.Q52304046
Ligand docking to proteins with discrete side-chain flexibility.Q52383197
General and targeted statistical potentials for protein-ligand interactions.Q52981145
Multitarget Drug Discovery and Polypharmacology.Q53376374
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.Q53678858
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy functionQ56885198
Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An OverviewQ58719254
Can you teach old drugs new tricks?Q59080940
Phase Transition for a Hard Sphere SystemQ60395801
On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structureQ72593914
Thermodynamic contributions of the ordered water molecule in HIV-1 proteaseQ73442110
The physicochemical challenges of designing multiple ligandsQ80048530
A QXP-based multistep docking procedure for accurate prediction of protein-ligand complexesQ83372797
Targeting multiple kinases in glioblastoma multiformeQ83395665
Challenges and opportunities of drug repositioningQ86587232
Supervised Molecular Dynamics (SuMD) Approaches in Drug DesignQ90434913
Ginkgolic Acid is a Multi-Target Inhibitor of Key Enzymes in Pro-Inflammatory Lipid Mediator BiosynthesisQ92403172
Novel promising 4-anilinoquinazoline-based derivatives as multi-target RTKs inhibitors: Design, molecular docking, synthesis, and antitumor activities in vitro and vivoQ93130382
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic LiquidsQ99192955
SODOCK: swarm optimization for highly flexible protein-ligand docking.Q51091845
Scoring ligand similarity in structure-based virtual screening.Q51806309
Binding estimation after refinement, a new automated procedure for the refinement and rescoring of docked ligands in virtual screening.Q51829468
Improved protein-ligand docking using GOLDQ29616787
The MARTINI force field: coarse grained model for biomolecular simulationsQ29617215
Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screeningQ29617343
Monte Carlo replica-exchange based ensemble docking of protein conformationsQ30398315
From in silico target prediction to multi-target drug design: current databases, methods and applicationsQ30403222
FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structureQ30420637
Ligand binding to proteins: the binding landscape modelQ30428684
Novel paradigms for drug discovery: computational multitarget screeningQ30662767
High-throughput docking for lead generationQ30663788
Molecular recognition and docking algorithmsQ31130825
Combining docking and molecular dynamic simulations in drug designQ33245994
pso@autodock: a fast flexible molecular docking program based on Swarm intelligenceQ33305123
Results of dasatinib therapy in patients with early chronic-phase chronic myeloid leukemiaQ33387517
Ginkgolic acid inhibits protein SUMOylation by blocking formation of the E1-SUMO intermediateQ33412950
Current combination chemotherapy regimens for metastatic breast cancerQ33516194
A phase II study of flavopiridol (Alvocidib) in combination with docetaxel in refractory, metastatic pancreatic cancerQ33739625
Targeting the cancer kinome through polypharmacologyQ33893019
Integrating structure-based and ligand-based approaches for computational drug designQ33893108
Computer-aided identification of Trypanosoma brucei uridine diphosphate galactose 4'-epimerase inhibitors: toward the development of novel therapies for African sleeping sicknessQ33954211
Chemical genetics strategy identifies an HCV NS5A inhibitor with a potent clinical effectQ34022149
Synthesis, biological evaluation, and molecular modeling of donepezil and N-[(5-(benzyloxy)-1-methyl-1H-indol-2-yl)methyl]-N-methylprop-2-yn-1-amine hybrids as new multipotent cholinesterase/monoamine oxidase inhibitors for the treatment of [...]Q34056563
Molecular dynamics simulations and drug discoveryQ34061019
Polypharmacology: drug discovery for the futureQ34319906
Advances and challenges in protein-ligand dockingQ34377911
The GROMOS software for biomolecular simulation: GROMOS05.Q34457783
A new force field (ECEPP-05) for peptides, proteins, and organic moleculesQ34565535
Development and validation of a modular, extensible docking program: DOCK 5.Q34588100
Phase II study of dasatinib in patients with metastatic castration-resistant prostate cancerQ34613941
ABT-869, a multitargeted receptor tyrosine kinase inhibitor: inhibition of FLT3 phosphorylation and signaling in acute myeloid leukemiaQ35751114
From magic bullets to designed multiple ligandsQ35848618
Phase 1 clinical results with tandutinib (MLN518), a novel FLT3 antagonist, in patients with acute myelogenous leukemia or high-risk myelodysplastic syndrome: safety, pharmacokinetics, and pharmacodynamicsQ35848830
Multiple target drug cocktail design for attacking the core network markers of four cancers using ligand-based and structure-based virtual screening methodsQ35872435
Multi-functional drugs for various CNS targets in the treatment of neurodegenerative disordersQ35998174
How to develop a successful cancer drug--molecules to medicines or targets to treatments?Q36069293
Target flexibility in molecular recognitionQ36266696
Designed multiple ligands. An emerging drug discovery paradigmQ36284452
Molecular dynamics: survey of methods for simulating the activity of proteinsQ36472758
Antileukemic effects of the novel, mutant FLT3 inhibitor NVP-AST487: effects on PKC412-sensitive and -resistant FLT3-expressing cellsQ37003553
Multi-target-directed ligands to combat neurodegenerative diseasesQ37052982
Pazopanib, a potent orally administered small-molecule multitargeted tyrosine kinase inhibitor for renal cell carcinomaQ37071204
Early clinical studies of novel therapies for thyroid cancersQ37172796
How many modes of action should an antibiotic have?Q37214061
Imatinib treatment for gastrointestinal stromal tumour (GIST).Q37334993
Designing multiple ligands - medicinal chemistry strategies and challengesQ37387562
Activity of the multikinase inhibitor dasatinib against ovarian cancer cellsQ37424063
In-silico approaches to multi-target drug discovery : computer aided multi-target drug design, multi-target virtual screeningQ37707220
The role of fragment-based and computational methods in polypharmacology.Q37921883
Polypharmacology in a single drug: multitarget drugsQ38081536
Protein-ligand docking in the new millennium--a retrospective of 10 years in the fieldQ38093314
Polypharmacology - foe or friend?Q38126927
Polypharmacology: challenges and opportunities in drug discoveryQ38221607
Systems biology brings new dimensions for structure-based drug designQ38233920
In silico methods to address polypharmacology: current status, applications and future perspectivesQ38689965
Computational Multitarget Drug Design.Q38760828
PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand dockingQ39026290
A comprehensive map of molecular drug targets.Q39026969
Antitumor activities of the targeted multi-tyrosine kinase inhibitor lenvatinib (E7080) against RET gene fusion-driven tumor modelsQ39125714
The inevitable QSAR renaissanceQ39681298
The RET kinase inhibitor NVP-AST487 blocks growth and calcitonin gene expression through distinct mechanisms in medullary thyroid cancer cellsQ40105425
A New Method for Navigating Optimal Direction for Pulling Ligand from Binding Pocket: Application to Ranking Binding Affinity by Steered Molecular DynamicsQ40288332
The in vitro and in vivo effects of JNJ-7706621: a dual inhibitor of cyclin-dependent kinases and aurora kinasesQ40365711
CHIR-258, a novel, multitargeted tyrosine kinase inhibitor for the potential treatment of t(4;14) multiple myeloma.Q40480723
A combination of cisplatin-eluting gelatin microspheres and flavopiridol enhances anti-tumour effects in a rabbit VX2 liver tumour modelQ41993498
New pharmacological developments in the treatment of hepatocellular cancerQ43234592
Phase I and biomarker study of ABT-869, a multiple receptor tyrosine kinase inhibitor, in patients with refractory solid malignanciesQ43282879
Hematologic and cytogenetic responses to imatinib mesylate in chronic myelogenous leukemiaQ43899710
Computational drug design accommodating receptor flexibility: the relaxed complex schemeQ43992973
Phase II study of flavopiridol in patients with advanced colorectal cancerQ44525933
A multiple-start Monte Carlo docking method.Q44677796
Water network perturbation in ligand binding: adenosine A(2A) antagonists as a case study.Q44760042
FlexX-Scan: fast, structure-based virtual screeningQ45070169
In vivo target modulation and biological activity of CHIR-258, a multitargeted growth factor receptor kinase inhibitor, in colon cancer modelsQ46173286
CHIR-258: a potent inhibitor of FLT3 kinase in experimental tumor xenograft models of human acute myelogenous leukemiaQ46610628
N-Methyl-N-((1-methyl-5-(3-(1-(2-methylbenzyl)piperidin-4-yl)propoxy)-1H-indol-2-yl)methyl)prop-2-yn-1-amine, a new cholinesterase and monoamine oxidase dual inhibitor.Q48449256
Deciphering the Complexity of Ligand-Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations.Q50525174
P577publication date2020-04-23
P1433published inDrug Development ResearchQ15749332
P1476titleProspects of multitarget drug designing strategies by linking molecular docking and molecular dynamics to explore the protein-ligand recognition process

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Q100430222Recent progress on cheminformatics approaches to epigenetic drug discoverycites workP2860

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