Combining Molecular Dynamics and Docking Simulations to Develop Targeted Protocols for Performing Optimized Virtual Screening Campaigns on the hTRPM8 Channel

Background: There is an increasing interest in TRPM8 ligands of medicinal interest, the rational design of which can be nowadays supported by structure-based in silico studies based on the recently resolved TRPM8 structures. Methods: The study involves the generation of a reliable hTRPM8 homology model, the reliability of which was assessed by a 1.0 μs MD simulation which was also used to generate multiple receptor conformations for the following structure-based virtual screening (VS) campaigns; docking simulations utilized different programs and involved all monomers of the selected frames; the so computed docking scores were combined by consensus approaches based on the EFO algorithm. Results: The obtained models revealed very satisfactory performances; LiGen™ provided the best results among the tested docking programs; the combination of docking results from the four monomers elicited a markedly beneficial effect on the computed consensus models. Conclusions: The generated hTRPM8 model appears to be amenable for successful structure-based VS studies; cross-talk modulating effects between interacting monomers on the binding sites can be accounted for by combining docking simulations as performed on all the monomers; this strategy can have general applicability for docking simulations involving quaternary protein structures with multiple identical binding pockets.

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A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0

International Journal of Molecular Sciences ◽

10.3390/ijms21145152 ◽

2020 ◽

Vol 21 (14) ◽

pp. 5152 ◽

Cited By ~ 5

Author(s):

Silvia Gervasoni ◽

Giulio Vistoli ◽

Carmine Talarico ◽

Candida Manelfi ◽

Andrea R. Beccari ◽

...

Keyword(s):

Virtual Screening ◽

Drug Repurposing ◽

Protein Targets ◽

In Silico Studies ◽

Allosteric Sites ◽

Binding Pockets ◽

Novel Strategy ◽

Better Than ◽

Comprehensive Mapping

(1) Background: Virtual screening studies on the therapeutically relevant proteins of the severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) require a detailed characterization of their druggable binding sites, and, more generally, a convenient pocket mapping represents a key step for structure-based in silico studies; (2) Methods: Along with a careful literature search on SARS-CoV-2 protein targets, the study presents a novel strategy for pocket mapping based on the combination of pocket (as performed by the well-known FPocket tool) and docking searches (as performed by PLANTS or AutoDock/Vina engines); such an approach is implemented by the Pockets 2.0 plug-in for the VEGA ZZ suite of programs; (3) Results: The literature analysis allowed the identification of 16 promising binding cavities within the SARS-CoV-2 proteins and the here proposed approach was able to recognize them showing performances clearly better than those reached by the sole pocket detection; and (4) Conclusions: Even though the presented strategy should require more extended validations, this proved successful in precisely characterizing a set of SARS-CoV-2 druggable binding pockets including both orthosteric and allosteric sites, which are clearly amenable for virtual screening campaigns and drug repurposing studies. All results generated by the study and the Pockets 2.0 plug-in are available for download.

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Combining Different Docking Engines and Consensus Strategies to Design and Validate Optimized Virtual Screening Protocols for the SARS-CoV-2 3CL Protease

Molecules ◽

10.3390/molecules26040797 ◽

2021 ◽

Vol 26 (4) ◽

pp. 797

Author(s):

Candida Manelfi ◽

Jonas Gossen ◽

Silvia Gervasoni ◽

Carmine Talarico ◽

Simone Albani ◽

...

Keyword(s):

Virtual Screening ◽

Binding Modes ◽

Training Set ◽

Docking Simulations ◽

Rational Development ◽

Consensus Models ◽

Multiple Binding ◽

Innovative Idea ◽

3Cl Protease

The 3CL-Protease appears to be a very promising medicinal target to develop anti-SARS-CoV-2 agents. The availability of resolved structures allows structure-based computational approaches to be carried out even though the lack of known inhibitors prevents a proper validation of the performed simulations. The innovative idea of the study is to exploit known inhibitors of SARS-CoV 3CL-Pro as a training set to perform and validate multiple virtual screening campaigns. Docking simulations using four different programs (Fred, Glide, LiGen, and PLANTS) were performed investigating the role of both multiple binding modes (by binding space) and multiple isomers/states (by developing the corresponding isomeric space). The computed docking scores were used to develop consensus models, which allow an in-depth comparison of the resulting performances. On average, the reached performances revealed the different sensitivity to isomeric differences and multiple binding modes between the four docking engines. In detail, Glide and LiGen are the tools that best benefit from isomeric and binding space, respectively, while Fred is the most insensitive program. The obtained results emphasize the fruitful role of combining various docking tools to optimize the predictive performances. Taken together, the performed simulations allowed the rational development of highly performing virtual screening workflows, which could be further optimized by considering different 3CL-Pro structures and, more importantly, by including true SARS-CoV-2 3CL-Pro inhibitors (as learning set) when available.

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In Silico Studies on Acetylcholine Receptor Subunit Alpha-L1 for Proposal of Novel Insecticides against Aphis craccivora

Chemistry Proceedings ◽

10.3390/ecsoc-24-08366 ◽

2020 ◽

Vol 3 (1) ◽

pp. 8

Author(s):

Ana Borota ◽

Luminita Crisan ◽

Alina Bora ◽

Simona Funar-Timofei

Keyword(s):

Acetylcholine Receptor ◽

Rational Design ◽

3D Structure ◽

Homology Model ◽

Plant Viruses ◽

Aphis Craccivora ◽

Interaction Patterns ◽

Receptor Subunit ◽

Screening Experiments ◽

In Silico Studies

: Aphis craccivora is an aphid which damages many species of plants and is also a vector for numerous plant viruses. Since neonicotinoids are a well-known class of effective insecticides with less toxicity against mammals and other vertebrates, a small dataset of compounds retrieved from the literature based on similarity to highly active neonicotinoids was used. Thus, homology modeling was involved in the building of the 3D structure of the acetylcholine receptor subunit alpha-L1 of Aphis craccivora. The homology model was involved in virtual screening experiments using the FRED docking tool of the OpenEye software. The aforementioned dataset was used to explore the intermolecular ligand–target interaction patterns for a rational design of desired and relatively safe insecticides.

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Comprehensive in silico Study of GLUT10: Prediction of Possible Substrate Binding Sites and Interacting Molecules

Current Pharmaceutical Biotechnology ◽

10.2174/1389201020666190613152030 ◽

2020 ◽

Vol 21 (2) ◽

pp. 117-130 ◽

Cited By ~ 1

Author(s):

Mohammad J. Hosen ◽

Mahmudul Hasan ◽

Sourav Chakraborty ◽

Ruhshan A. Abir ◽

Abdullah Zubaer ◽

...

Keyword(s):

Virtual Screening ◽

Binding Site ◽

Glucose Transporter ◽

Substrate Binding ◽

Mutation Screening ◽

Homology Model ◽

Connective Tissue Disorder ◽

Crystallographic Structure ◽

Substrate Binding Site

Objectives: The Arterial Tortuosity Syndrome (ATS) is an autosomal recessive connective tissue disorder, mainly characterized by tortuosity and stenosis of the arteries with a propensity towards aneurysm formation and dissection. It is caused by mutations in the SLC2A10 gene that encodes the facilitative glucose transporter GLUT10. The molecules transported by and interacting with GLUT10 have still not been unambiguously identified. Hence, the study attempts to identify both the substrate binding site of GLUT10 and the molecules interacting with this site. Methods: As High-resolution X-ray crystallographic structure of GLUT10 was not available, 3D homology model of GLUT10 in open conformation was constructed. Further, molecular docking and bioinformatics investigation were employed. Results and Discussion: Blind docking of nine reported potential in vitro substrates with this 3D homology model revealed that substrate binding site is possibly made with PRO531, GLU507, GLU437, TRP432, ALA506, LEU519, LEU505, LEU433, GLN525, GLN510, LYS372, LYS373, SER520, SER124, SER533, SER504, SER436 amino acid residues. Virtual screening of all metabolites from the Human Serum Metabolome Database and muscle metabolites from Human Metabolite Database (HMDB) against the GLUT10 revealed possible substrates and interacting molecules for GLUT10, which were found to be involved directly or partially in ATS progression or different arterial disorders. Reported mutation screening revealed that a highly emergent point mutation (c. 1309G>A, p. Glu437Lys) is located in the predicted substrate binding site region. Conclusion: Virtual screening expands the possibility to explore more compounds that can interact with GLUT10 and may aid in understanding the mechanisms leading to ATS.

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Identification of a Potential Inhibitor Targeting MurC Ligase of the Drug Resistant Pseudomonas aeruginosa Strain through Structure-Based Virtual Screening Approach and In Vitro Assay

Current Pharmaceutical Biotechnology ◽

10.2174/1389201020666190719123133 ◽

2019 ◽

Vol 20 (14) ◽

pp. 1203-1212

Author(s):

Abdelmonaem Messaoudi ◽

Manel Zoghlami ◽

Zarrin Basharat ◽

Najla Sadfi-Zouaoui

Keyword(s):

Pseudomonas Aeruginosa ◽

Virtual Screening ◽

Homology Model ◽

Generation Cephalosporin ◽

World Health ◽

Resistant Bacteria ◽

Antimicrobial Drugs ◽

Vitro Assay ◽

Priority List

Background & Objective: Pseudomonas aeruginosa shows resistance to a large number of antibiotics, including carbapenems and third generation cephalosporin. According to the World Health Organization global report published in February 2017, Pseudomonas aeruginosa is on the priority list among resistant bacteria, for which new antibiotics are urgently needed. Peptidoglycan serves as a good target for the discovery of novel antimicrobial drugs. Methods: Biosynthesis of peptidoglycan is a multi-step process involving four mur enzymes. Among these enzymes, UDP-N-acetylmuramate-L-alanine ligase (MurC) is considered to be an excellent target for the design of new classes of antimicrobial inhibitors in gram-negative bacteria. Results: In this study, a homology model of Pseudomonas aeruginosa MurC ligase was generated and used for virtual screening of chemical compounds from the ZINC Database. The best screened inhibitor i.e. N, N-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazole-5-sulfonamide was then validated experimentally through inhibition assay. Conclusion: The presented results based on combined computational and in vitro analysis open up new horizons for the development of novel antimicrobials against this pathogen.

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Synthesis of Coumarin Derivatives as Versatile Scaffolds for GSK-3β Enzyme Inhibition

Current Topics in Medicinal Chemistry ◽

10.2174/1568026619666191019105349 ◽

2020 ◽

Vol 20 (2) ◽

pp. 153-160 ◽

Cited By ~ 1

Author(s):

Carla S. Francisco ◽

Clara L. Javarini ◽

Iatahanderson de S. Barcelos ◽

Pedro A.B. Morais ◽

Heberth de Paula ◽

...

Keyword(s):

Kinase Inhibitors ◽

Glycogen Synthase ◽

Synthetic Methods ◽

Kinase Assay ◽

Crystallographic Structure ◽

Coumarin Derivatives ◽

Enzymatic Production ◽

Docking Simulations ◽

In Silico Studies ◽

Gsk 3Β

Background: Glycogen synthase kinase-3 (GSK-3) is involved in the phosphorylation and inactivation of glycogen synthase. GSK-3 inhibitors have been associated with a variety of diseases, including Alzheimer´s disease (AD), diabetes type II, neurologic disorders, and cancer. The inhibition of GSK-3β isoforms is likely to represent an effective strategy against AD. Objective: The present work aimed to design and synthesize coumarin derivatives to explore their potential as GSK-3β kinase inhibitors. Method: The through different synthetic methods were used to prepare coumarin derivatives. The GSK-3β activity was measured through the ADP-Glo™ Kinase Assay, which quantifies the kinasedependent enzymatic production of ADP from ATP, using a coupled-luminescence-based reaction. A docking study was performed by using the crystallographic structure of the staurosporine/GSK-3β complex [Protein Data Bank (PDB) code: 1Q3D]. Results: The eleven coumarin derivatives were obtained and evaluated as potential GSK-3β inhibitors. Additionally, in silico studies were performed. The results revealed that the compounds 5c, 5d, and 6b inhibited GSK-3β enzymatic activity by 38.97–49.62% at 1 mM. The other coumarin derivatives were tested at 1 mM, 1 µM, and 1 nM concentrations and were shown to be inhibitor candidates, with significant IC50 (1.224–6.875 µM) values, except for compound 7c (IC50 = 10.809 µM). Docking simulations showed polar interactions between compound 5b and Lys85 and Ser203, clarifying the mechanism of the most potent activity. Conclusion: The coumarin derivatives 3a and 5b, developed in this study, showed remarkable activity as GSK-3β inhibitors.

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Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Molecules ◽

10.3390/molecules26010198 ◽

2021 ◽

Vol 26 (1) ◽

pp. 198

Author(s):

Lijun Lang ◽

Alberto Perez

Keyword(s):

Bayesian Inference ◽

Virtual Screening ◽

Statistical Mechanics ◽

Small Molecules ◽

Rational Design ◽

Driving Forces ◽

Peptide Inhibitors ◽

Atomistic Simulations ◽

Binding Mechanism ◽

Intrinsically Disordered

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).

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Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations

Scientific Reports ◽

10.1038/s41598-021-84488-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Gert-Jan Bekker ◽

Ikuo Fukuda ◽

Junichi Higo ◽

Yoshifumi Fukunishi ◽

Narutoshi Kamiya

Keyword(s):

Ligand Binding ◽

Cancer Progression ◽

Hydrophobic Interactions ◽

Binding Mechanism ◽

Docking Simulations ◽

Large Conformational Change ◽

Binding Pockets ◽

Dynamic Docking ◽

Site Binding ◽

Apo State

AbstractWe have performed multicanonical molecular dynamics (McMD) based dynamic docking simulations to study and compare the binding mechanism between two medium-sized inhibitors (ABT-737 and WEHI-539) that bind to the cryptic site of Bcl-xL, by exhaustively sampling the conformational and configurational space. Cryptic sites are binding pockets that are transiently formed in the apo state or are induced upon ligand binding. Bcl-xL, a pro-survival protein involved in cancer progression, is known to have a cryptic site, whereby the shape of the pocket depends on which ligand is bound to it. Starting from the apo-structure, we have performed two independent McMD-based dynamic docking simulations for each ligand, and were able to obtain near-native complex structures in both cases. In addition, we have also studied their interactions along their respective binding pathways by using path sampling simulations, which showed that the ligands form stable binding configurations via predominantly hydrophobic interactions. Although the protein started from the apo state, both ligands modulated the pocket in different ways, shifting the conformational preference of the sub-pockets of Bcl-xL. We demonstrate that McMD-based dynamic docking is a powerful tool that can be effectively used to study binding mechanisms involving a cryptic site, where ligand binding requires a large conformational change in the protein to occur.

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