1
|
Kumari D, Jamwal V, Singh A, Singh SK, Mujwar S, Ansari MY, Singh K. Repurposing FDA approved drugs against Sterol C-24 methyltransferase of Leishmania donovani: A dual in silico and in vitro approach. Acta Trop 2024; 258:107338. [PMID: 39084482 DOI: 10.1016/j.actatropica.2024.107338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 07/08/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
Abstract
Leishmaniasis is a disease caused by the parasite Leishmania donovani affecting populations belonging to developing countries. The present study explores drug repurposing as an innovative strategy to identify new uses for approved clinical drugs, reducing the time and cost required for drug discovery. The three-dimensional structure of Leishmania donovani Sterol C-24 methyltransferase (LdSMT) was modeled and 1615 FDA-approved drugs from the ZINC database were computationally screened to identify the potent leads. Fulvestrant, docetaxel, indocyanine green, and iohexol were shortlisted as potential leads with the highest binding affinity and fitness scores for the concerned pathogenic receptor. Molecular dynamic simulation studies showed that the macromolecular complexes of indocyanine green and iohexol with LdSMT remained stable throughout the simulation and can be further evaluated experimentally for developing an effective drug. The proposed leads have further demonstrated promising safety profiles during cytotoxicity analysis on the J774.A1 macrophage cell line. Mechanistic analysis with these two drugs also revealed significant morphological alterations in the parasite, along with reduced intracellular parasitic load. Overall, this study demonstrates the potential of drug repurposing in identifying new treatments for leishmaniasis and other diseases affecting developing countries, highlighting the importance of considering approved clinical drugs for new applications.
Collapse
Affiliation(s)
- Diksha Kumari
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vishwani Jamwal
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ajeet Singh
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; Pharmacology Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India
| | - Shashank K Singh
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; Pharmacology Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India
| | - Somdutt Mujwar
- Chitkara College of Pharmacy, Chitkara University, Rajpura, 140401, Punjab, India
| | - Md Yousuf Ansari
- M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Kuljit Singh
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
2
|
Boittier E, Töpfer K, Devereux M, Meuwly M. Kernel-Based Minimal Distributed Charges: A Conformationally Dependent ESP-Model for Molecular Simulations. J Chem Theory Comput 2024. [PMID: 39230188 DOI: 10.1021/acs.jctc.4c00759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
A kernel-based method (kernelized minimal distributed charge model (kMDCM)) to represent the molecular electrostatic potential (ESP) in terms of off-center point charges is introduced. The positions of the charges adapt to the molecular geometry and allow the description of intramolecular charge flow. Using Gaussian kernels and atom-atom distances as the features, the ESPs for water and methanol are shown to improve by at least a factor of 2 compared with point charge models fit to an ensemble of structures. The conformationally fluctuating molecular dipole moment of water is reproduced almost twice as accurately using kMDCM compared with static PCs, despite not fitting to the dipole directly. The role of hyperparameters in the kernelization is investigated and their implication on model performance and simulation stability is discussed. Combining kMDCM for the electrostatics and reproducing kernels for the bonded terms allows energy-conserving simulations of 2000 water molecules with periodic boundary conditions on the nanosecond time scale. These MD simulations sample geometries outside the training set but remain stable, which demonstrates the robustness of the model and its implementation.
Collapse
Affiliation(s)
- Eric Boittier
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Mike Devereux
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| |
Collapse
|
3
|
Kaveh S, Mani-Varnosfaderani A, Neiband MS. Deriving general structure-activity/selectivity relationship patterns for different subfamilies of cyclin-dependent kinase inhibitors using machine learning methods. Sci Rep 2024; 14:15315. [PMID: 38961127 PMCID: PMC11222421 DOI: 10.1038/s41598-024-66173-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
Cyclin-dependent kinases (CDKs) play essential roles in regulating the cell cycle and are among the most critical targets for cancer therapy and drug discovery. The primary objective of this research is to derive general structure-activity relationship (SAR) patterns for modeling the selectivity and activity levels of CDK inhibitors using machine learning methods. To accomplish this, 8592 small molecules with different binding affinities to CDK1, CDK2, CDK4, CDK5, and CDK9 were collected from Binding DB, and a diverse set of descriptors was calculated for each molecule. The supervised Kohonen networks (SKN) and counter propagation artificial neural networks (CPANN) models were trained to predict the activity levels and therapeutic targets of the molecules. The validity of models was confirmed through tenfold cross-validation and external test sets. Using selected sets of molecular descriptors (e.g. hydrophilicity and total polar surface area) we derived activity and selectivity maps to elucidate local regions in chemical space for active and selective CDK inhibitors. The SKN models exhibited prediction accuracies ranging from 0.75 to 0.94 for the external test sets. The developed multivariate classifiers were used for ligand-based virtual screening of 2 million random molecules of the PubChem database, yielding areas under the receiver operating characteristic curves ranging from 0.72 to 1.00 for the SKN model. Considering the persistent challenge of achieving CDK selectivity, this research significantly contributes to addressing the issue and underscores the paramount importance of developing drugs with minimized side effects.
Collapse
Affiliation(s)
- Sara Kaveh
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran
| | - Ahmad Mani-Varnosfaderani
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran.
| | - Marzieh Sadat Neiband
- Department of Chemistry, Payame Noor University (PNU), P.O. Box 19395-4697, Tehran, Iran
| |
Collapse
|
4
|
Wang Y, Wang D, Dong B, Hao J, Jia X, Zhou H. Potential Candidate Molecule of Photosystem II Inhibitor Herbicide-Brassicanate A Sulfoxide. Int J Mol Sci 2024; 25:2400. [PMID: 38397082 PMCID: PMC10889811 DOI: 10.3390/ijms25042400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Brassicanate A sulfoxide, a secondary metabolite of broccoli, exhibited the inhibition of weed growth, but its mechanism of action on weeds remains unclear. To elucidate the mechanism by which brassicanate A sulfoxide suppresses weeds, this study explores the interaction between brassicanate A sulfoxide and the photosystem II D1 protein through molecular docking and molecular dynamics simulations. This research demonstrates that brassicanate A sulfoxide interacts with the photosystem II D1 protein by forming hydrogen bonds with Phe-261 and His-214. The successful expression of the photosystem II D1 protein in an insect cell/baculovirus system validated the molecular docking and dynamics simulations. Biolayer interferometry experiments elucidated that the affinity constant of brassicanate A sulfoxide with photosystem II was 2.69 × 10-3 M, suggesting that brassicanate A sulfoxide can stably bind to the photosystem II D1 protein. The findings of this study contribute to the understanding of the mode of action of brassicanate A sulfoxide and also aid in the development of natural-product-based photosynthesis-inhibiting herbicides.
Collapse
Affiliation(s)
| | | | | | | | | | - Hongyou Zhou
- Key Laboratory of Biopesticide Creation and Resource Utilization for Autonomous Region Higher Education Institutions, College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010018, China
| |
Collapse
|
5
|
Das S, Merz KM. Molecular Gas-Phase Conformational Ensembles. J Chem Inf Model 2024; 64:749-760. [PMID: 38206321 DOI: 10.1021/acs.jcim.3c01309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Accurately determining the global minima of a molecular structure is important in diverse scientific fields, including drug design, materials science, and chemical synthesis. Conformational search engines serve as valuable tools for exploring the extensive conformational space of molecules and for identifying energetically favorable conformations. In this study, we present a comparison of Auto3D, CREST, Balloon, and ETKDG (from RDKit), which are freely available conformational search engines, to evaluate their effectiveness in locating global minima. These engines employ distinct methodologies, including machine learning (ML) potential-based, semiempirical, and force field-based approaches. To validate these methods, we propose the use of collisional cross-section (CCS) values obtained from ion mobility-mass spectrometry studies. We hypothesize that experimental gas-phase CCS values can provide experimental evidence that we likely have the global minimum for a given molecule. To facilitate this effort, we used our gas-phase conformation library (GPCL) which currently consists of the full ensembles of 20 small molecules and can be used by the community to validate any conformational search engine. Further members of the GPCL can be readily created for any molecule of interest using our standard workflow used to compute CCS values, expanding the ability of the GPCL in validation exercises. These innovative validation techniques enhance our understanding of the conformational landscape and provide valuable insights into the performance of conformational generation engines. Our findings shed light on the strengths and limitations of each search engine, enabling informed decisions for their utilization in various scientific fields, where accurate molecular structure determination is crucial for understanding biological activity and designing targeted interventions. By facilitating the identification of reliable conformations, this study significantly contributes to enhancing the efficiency and accuracy of molecular structure determination, with particular focus on metabolite structure elucidation. The findings of this research also provide valuable insights for developing effective workflows for predicting the structures of unknown compounds with high precision.
Collapse
Affiliation(s)
- Susanta Das
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| |
Collapse
|
6
|
Stylianakis I, Zervos N, Lii JH, Pantazis DA, Kolocouris A. Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory. J Comput Aided Mol Des 2023; 37:607-656. [PMID: 37597063 PMCID: PMC10618395 DOI: 10.1007/s10822-023-00513-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 08/21/2023]
Abstract
We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.
Collapse
Affiliation(s)
- Ioannis Stylianakis
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Nikolaos Zervos
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Jenn-Huei Lii
- Department of Chemistry, National Changhua University of Education, Changhua City, Taiwan
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Antonios Kolocouris
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece.
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece.
| |
Collapse
|
7
|
Rampogu S, Shaik MR, Khan M, Khan M, Oh TH, Shaik B. CBPDdb: a curated database of compounds derived from Coumarin-Benzothiazole-Pyrazole. Database (Oxford) 2023; 2023:baad062. [PMID: 37702993 PMCID: PMC10498939 DOI: 10.1093/database/baad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/01/2023] [Accepted: 08/26/2023] [Indexed: 09/14/2023]
Abstract
The present article describes the building of a small-molecule web server, CBPDdb, employing R-shiny. For the generation of the web server, three compounds were chosen, namely coumarin, benzothiazole and pyrazole, and their derivatives were curated from the literature. The two-dimensional (2D) structures were drawn using ChemDraw, and the .sdf file was created employing Discovery Studio Visualizer v2017. These compounds were read on the R-shiny app using ChemmineR, and the dataframe consisting of a total of 1146 compounds was generated and manipulated employing the dplyr package. The web server is provided with JSME 2D sketcher. The descriptors of the compounds are obtained using propOB with a filter. The users can download the filtered data in the .csv and .sdf formats, and the entire dataset of a compound can be downloaded in .sdf format. This web server facilitates the researchers to screen plausible inhibitors for different diseases. Additionally, the method used in building the web server can be adapted for developing other small-molecule databases (web servers) in RStudio. Database URL: https://srampogu.shinyapps.io/CBPDdb_Revised/.
Collapse
Affiliation(s)
| | - Mohammed Rafi Shaik
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Merajuddin Khan
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mujeeb Khan
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Tae Hwan Oh
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Baji Shaik
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| |
Collapse
|
8
|
Talmazan RA, Podewitz M. PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent. J Chem Inf Model 2023; 63:5400-5407. [PMID: 37606893 PMCID: PMC10498442 DOI: 10.1021/acs.jcim.3c00798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Indexed: 08/23/2023]
Abstract
We introduce PyConSolv, a freely available Python package that automates the generation of conformers of metal- and nonmetal-containing complexes in explicit solvent, through classical molecular dynamics simulations. Using a streamlined workflow and interfacing with widely used computational chemistry software, PyConSolv is an all-in-one tool for the generation of conformers in any solvent. Input requirements are minimal; only the geometry of the structure and the desired solvent in xyz (XMOL) format are needed. The package can also account for charged systems, by including arbitrary counterions in the simulation. A bonded model parametrization is performed automatically, utilizing AmberTools, ORCA, and Multiwfn software packages. PyConSolv provides a selection of preparametrized solvents and counterions for use in classical molecular dynamics simulations. We show the applicability of our package on a number of (transition-metal-containing) systems. The software is provided open source and free of charge.
Collapse
Affiliation(s)
- R. A. Talmazan
- Institute
of Materials Chemistry, TU Wien, Getreidemarkt 9, A-1060 Wien, Austria
| | - M. Podewitz
- Institute
of Materials Chemistry, TU Wien, Getreidemarkt 9, A-1060 Wien, Austria
| |
Collapse
|
9
|
Darsaraee M, Kaveh S, Mani-Varnosfaderani A, Neiband MS. General structure-activity/selectivity relationship patterns for the inhibitors of the chemokine receptors (CCR1/CCR2/CCR4/CCR5) with application for virtual screening of PubChem database. J Biomol Struct Dyn 2023:1-19. [PMID: 37599469 DOI: 10.1080/07391102.2023.2248255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
CC chemokine receptors (CCRs) form a crucial subfamily of G protein-linked receptors that play a distinct role in the onset and progression of various life-threatening diseases. The main aim of this research is to derive general structure-activity relationship (SAR) patterns to describe the selectivity and activity of CCR inhibitors. To this end, a total of 7332 molecules related to the inhibition of CCR1, CCR2, CCR4, and CCR5 were collected from the Binding Database and analyzed using machine learning techniques. A diverse set of 450 molecular descriptors was calculated for each molecule, and the molecules were classified based on their therapeutic targets and activities. The variable importance in the projection (VIP) approach was used to select discriminatory molecular features, and classification models were developed using supervised Kohonen networks (SKN) and counter-propagation artificial neural networks (CPANN). The reliability and predictability of the models were estimated using 10-fold cross-validation, an external validation set, and an applicability domain approach. We were able to identify different sets of molecular descriptors for discriminating between active and inactive molecules and model the selectivity of inhibitors towards different CCRs. The sensitivities of the predictions for the external test set for the SKN models ranged from 0.827-0.873. Finally, the developed classification models were used to screen approximately 2 million random molecules from the PubChem database, with average values for areas under the receiver operating characteristic curves ranging from 0.78-0.96 for SKN models and 0.75-0.89 for CPANN models.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- M Darsaraee
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran
| | - S Kaveh
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran
| | - A Mani-Varnosfaderani
- Chemometrics and Cheminformatics Laboratory, Department of Analytical Chemistry, Tarbiat Modares University, Tehran, Iran
| | - M S Neiband
- Department of Chemistry, Payame Noor University (PNU), Tehran, Iran
| |
Collapse
|
10
|
Franca TC, Goncalves ADS, Bérubé C, Voyer N, Aubry N, LaPlante SR. Determining the Predominant Conformations of Mortiamides A-D in Solution Using NMR Data and Molecular Modeling Tools. ACS OMEGA 2023; 8:25832-25838. [PMID: 37521620 PMCID: PMC10373451 DOI: 10.1021/acsomega.3c01206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/07/2023] [Indexed: 08/01/2023]
Abstract
Macrocyclic peptidomimetics have been seriously contributing to our arsenal of drugs to combat diseases. The search for nature's discoveries led us to mortiamides A-D (found in a novel fungus from Northern Canada), which is a family of cyclic peptides that clearly have demonstrated impressive pharmaceutical potential. This prompted us to learn more about their solution-state properties as these are central for binding to target molecules. Here, we secured and isolated mortiamide D, and then acquired high-resolution nuclear magnetic resonance (NMR) data to learn more about its structure and dynamics attributes. Sets of two-dimensional NMR experiments provided atomic-level (through-bond and through-space) data to confirm the primary structure, and NMR-driven molecular dynamics (MD) simulations suggested that more than one predominant three-dimensional (3D) structure exist in solution. Further steps of MD simulations are consistent with the finding that the backbones of mortiamides A-C also have at least two prominent macrocyclic shapes, but the side-chain structures and dynamics differed significantly. Knowledge of these solution properties can be exploited for drug design and discovery.
Collapse
Affiliation(s)
- Tanos
C. C. Franca
- INRS
− Centre Armand-Frappier Santé Biotechnologie, Université de Québec, 531 Boulevard des Prairies, Laval, Quebec H7V 1B7, Canada
- Laboratory
of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, 22290-270 Rio de Janeiro, Brazil
- Department
of Chemistry, Faculty of Science, University
of Hradec Králové, Rokitanskeho 62, 50003 Hradec Králové, Czech Republic
| | - Arlan da Silva Goncalves
- Department
of Chemistry, Federal Institute of Espírito
Santo − Unit Vila Velha, 29106-010 Vila Velha, ES, Brazil
- PPGQUI
(Graduate Program in Chemistry), Federal
University of Espírito Santo, Av. Fernando Ferrari, 514,, 29075-910 Vitória, ES, Brazil
| | - Christopher Bérubé
- Departement
de Chimie and PROTEO, Faculté des Sciences et de Génie, Université Laval, 1045 Avenue de la Médecine, Québec, Quebec G1V OA6, Canada
| | - Normand Voyer
- Departement
de Chimie and PROTEO, Faculté des Sciences et de Génie, Université Laval, 1045 Avenue de la Médecine, Québec, Quebec G1V OA6, Canada
| | - Norman Aubry
- NMR
consultant of Steven R. LaPlante’s Lab, INRS − Centre
Armand-Frappier Santé Biotechnologie, Université de Québec, 531 Boulevard des Prairies, Laval, Quebec H7V 1B7, Canada
| | - Steven R. LaPlante
- INRS
− Centre Armand-Frappier Santé Biotechnologie, Université de Québec, 531 Boulevard des Prairies, Laval, Quebec H7V 1B7, Canada
| |
Collapse
|
11
|
Azad I, Khan T, Ahmad N, Khan AR, Akhter Y. Updates on drug designing approach through computational strategies: a review. Future Sci OA 2023; 9:FSO862. [PMID: 37180609 PMCID: PMC10167725 DOI: 10.2144/fsoa-2022-0085] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/12/2023] [Indexed: 05/16/2023] Open
Abstract
The drug discovery and development (DDD) process in pursuit of novel drug candidates is a challenging procedure requiring lots of time and resources. Therefore, computer-aided drug design (CADD) methodologies are used extensively to promote proficiency in drug development in a systematic and time-effective manner. The point in reference is SARS-CoV-2 which has emerged as a global pandemic. In the absence of any confirmed drug moiety to treat the infection, the science fraternity adopted hit and trial methods to come up with a lead drug compound. This article is an overview of the virtual methodologies, which assist in finding novel hits and help in the progression of drug development in a short period with a specific medicinal solution.
Collapse
Affiliation(s)
- Iqbal Azad
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Tahmeena Khan
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Naseem Ahmad
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Abdul Rahman Khan
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, UP, 2260025, India
| |
Collapse
|
12
|
Molecular Design and In-Silico Analysis of Trisubstituted Benzimidazole Derivatives as Ftsz Inhibitor. J CHEM-NY 2023. [DOI: 10.1155/2023/9307613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
Tuberculosis (TB) is the fastest spreading infectious disease and one of the top ten diseases that kill millions of people annually. The rapid spread of a multidrug-resistant strain of Mycobacterium tuberculosis leads to multidrug-resistance tuberculosis (MDR-TB), which is very difficult to treat. Filament temperature-sensitive protein ring-Z (Ftsz) protein could be the best target to inhibit bacterial cytokinesis. This research is conducted to predict the antitubercular activity of trisubstituted benzimidazole derivatives targeting FtsZ protein by an in-silico approach (molecular docking, pharmacokinetic parameter, drug likeliness, toxicity prediction, and biological activity prediction). Amine and aldehyde substitutions are used as primary scaffolds to design 20 trisubstituted benzimidazole derivatives for molecular docking. AutoDock vina v.1.2.0 software was used to predict the binding interaction between ligand and receptor (FtsZ, PDB ID : 1RQ7). The drug-likeliness properties and toxicity of ligands were predicted from SwissADMET and ToxiM web servers, respectively. Compound A15 (2,3,5,6-tetrafluoro-N1-{6-fluoro-5-[4-(1H-imidazole-1-yl) phenoxy]-1H-1,3-benzodiazol-2-yl} benzene-1,4-diamine) showed the best binding energy (ΔG = −10.2 kcal/mol/) along with four hydrogen bond interactions (GLY107, PHE180, ASP 184). Similarly, compounds A19 and A20 have the best binding score of −9.8 kcal/mol, with excellent pharmacokinetic parameters. It is found that the binding energy of all ligands (ΔG = −8.0 to −10.2 kcal/mol) is better than the reference compound Moxifloxacin (ΔG = −7.7 kcal/mol). None of the ligands violate Lipinski’s rule, but all ligands’ toxicity is slightly high (>0.8 score). It is reported that the amine-substituted benzimidazole derivatives have better binding energy than the aldehyde substitution. Therefore, it is concluded that compounds A19 and A20 can be the best candidate as Ftsz protein inhibitors but an in-vitro animal study and toxicity study are necessary to validate these data.
Collapse
|
13
|
Chang Y, Hawkins BA, Du JJ, Groundwater PW, Hibbs DE, Lai F. A Guide to In Silico Drug Design. Pharmaceutics 2022; 15:pharmaceutics15010049. [PMID: 36678678 PMCID: PMC9867171 DOI: 10.3390/pharmaceutics15010049] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022] Open
Abstract
The drug discovery process is a rocky path that is full of challenges, with the result that very few candidates progress from hit compound to a commercially available product, often due to factors, such as poor binding affinity, off-target effects, or physicochemical properties, such as solubility or stability. This process is further complicated by high research and development costs and time requirements. It is thus important to optimise every step of the process in order to maximise the chances of success. As a result of the recent advancements in computer power and technology, computer-aided drug design (CADD) has become an integral part of modern drug discovery to guide and accelerate the process. In this review, we present an overview of the important CADD methods and applications, such as in silico structure prediction, refinement, modelling and target validation, that are commonly used in this area.
Collapse
Affiliation(s)
- Yiqun Chang
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Bryson A. Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jonathan J. Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paul W. Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - David E. Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Correspondence:
| |
Collapse
|
14
|
Boumezber S, Yelekçi K. Screening of novel and selective inhibitors for neuronal nitric oxide synthase (nNOS) via structure-based drug design techniques. J Biomol Struct Dyn 2022; 41:3607-3629. [PMID: 35322764 DOI: 10.1080/07391102.2022.2054471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
NO, or nitric oxide, is produced by a family of enzymes called nitric oxide synthase (NOS) from L-arginine. NO regulates many physiological functions such as smooth muscle relaxation, immune defense, and memory function. The overproduction of NO by the neuronal isoform of nitric oxide synthase (nNOS) is implicated in neurodegeneration and neuropathic pain, making nNOS inhibition a promising therapeutic approach. Many developed nNOS inhibitors, generally L-arginine mimetics, have some issues in selectivity and bioavailability. According to earlier studies, targeting nNOS has the advantage of decreasing excess NO in the brain while avoiding the negative consequences of inhibiting the two isozymes: endothelial NOS (eNOS) and inducible NOS (iNOS). This study applied structure-based virtual screening, molecular docking, and molecular dynamics simulations to design potent and selective inhibitors against nNOS over related isoforms (eNOS and iNOS) using human X-ray crystal structures of the NOS isoforms. It was discovered that some compounds displayed a very good inhibitory potency for hnNOS and moderate selectivity for the other isozymes, eNOS and iNOS, in addition to good solubility and desirable physiochemical properties. The compounds which showed good stability and selectivity with nNOS, such as ZINC000013485422, can be interesting and informative guidance for designing more potent human nNOS inhibitors.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sarah Boumezber
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
| |
Collapse
|
15
|
Pavan M, Bassani D, Bolcato G, Bissaro M, Sturles M, Moro S. Computational strategies to identify new drug candidates against neuroinflammation. Curr Med Chem 2022; 29:4756-4775. [PMID: 35135446 DOI: 10.2174/0929867329666220208095122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 11/22/2022]
Abstract
The even more increasing application of computational approaches in these last decades has deeply modified the process of discovery and commercialization of new therapeutic entities. This is especially true in the field of neuroinflammation, in which both the peculiar anatomical localization and the presence of the blood-brain barrier makeit mandatory to finely tune the candidates' physicochemical properties from the early stages of the discovery pipeline. The aim of this review is therefore to provide a general overview to the readers about the topic of neuroinflammation, together with the most common computational strategies that can be exploited to discover and design small molecules controlling neuroinflammation, especially those based on the knowledge of the three-dimensional structure of the biological targets of therapeutic interest. The techniques used to describe the molecular recognition mechanisms, such as molecular docking and molecular dynamics, will therefore be eviscerated, highlighting their advantages and their limitations. Finally, we report several case studies in which computational methods have been applied in drug discovery on neuroinflammation, focusing on the last decade's research.
Collapse
Affiliation(s)
- Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Giovanni Bolcato
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Maicol Bissaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Mattia Sturles
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| |
Collapse
|
16
|
|
17
|
Meng J, Zhang L, Wang L, Li S, Xie D, Zhang Y, Liu H. TSSF-hERG: A machine-learning-based hERG potassium channel-specific scoring function for chemical cardiotoxicity prediction. Toxicology 2021; 464:153018. [PMID: 34757159 DOI: 10.1016/j.tox.2021.153018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/15/2021] [Accepted: 10/26/2021] [Indexed: 11/27/2022]
Abstract
The human ether-à-go-go-related gene (hERG) encodes the Kv11.1 voltage-gated potassium ion (K+) channel that conducts the rapidly activating delayed rectifier current (IKr) in cardiomyocytes to regulate the repolarization process. Some drugs, as blockers of hERG potassium channels, cannot be marketed due to prolonged QT intervals, as well known as cardiotoxicity. Predetermining the binding affinity values between drugs and hERG through in silico methods can greatly reduce the time and cost required for experimental verification. In this study, we collected 9,215 compounds with AutoDock Vina's docking structures as training set, and collected compounds from four references as test sets. A series of models for predicting the binding affinities of hERG blockers were built based on five machine learning algorithms and combinations of interaction features and ligand features. The model built by support vector regression (SVR) using the combination of all features achieved the best performance on both tenfold cross-validation and external verification, which was selected and named as TSSF-hERG (target-specific scoring function for hERG). TSSF-hERG is more accurate than the classic scoring function of AutoDock Vina and the machine-learning-based generic scoring function RF-Score, with a Pearson's correlation coefficient (Rp) of 0.765, a Spearman's rank correlation coefficient (Rs) of 0.757, a root-mean-square error (RMSE) of 0.585 in a tenfold cross-validation study. All results demonstrated that TSSF-hERG would be useful for improving the power of binding affinity prediction between hERG and compounds, which can be further used for prediction or virtual screening of the hERG-related cardiotoxicity of drug candidates.
Collapse
Affiliation(s)
- Jinhui Meng
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Li Zhang
- School of Life Science, Liaoning University, Shenyang, 110036, China; Technology Innovation Center for Computer Simulating and Information Processing of Bio-macromolecules of Liaoning Province, Shenyang, 110036, China; Engineering Laboratory for Molecular Simulation and Designing of Drug Molecules of Liaoning, Shenyang, 110036, China
| | - Lianxin Wang
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Shimeng Li
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Di Xie
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Yuxi Zhang
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Hongsheng Liu
- Technology Innovation Center for Computer Simulating and Information Processing of Bio-macromolecules of Liaoning Province, Shenyang, 110036, China; Engineering Laboratory for Molecular Simulation and Designing of Drug Molecules of Liaoning, Shenyang, 110036, China; School of Pharmacy, Liaoning University, Shenyang, 110036, China.
| |
Collapse
|
18
|
Sharma S, Bhatia V. Appraisal of the Role of In silico Methods in Pyrazole Based Drug Design. Mini Rev Med Chem 2021; 21:204-216. [PMID: 32875985 DOI: 10.2174/1389557520666200901184146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/19/2020] [Accepted: 07/06/2020] [Indexed: 11/22/2022]
Abstract
Pyrazole and its derivatives are a pharmacologically and significantly active scaffolds that have innumerable physiological and pharmacological activities. They can be very good targets for the discovery of novel anti-bacterial, anti-cancer, anti-inflammatory, anti-fungal, anti-tubercular, antiviral, antioxidant, antidepressant, anti-convulsant and neuroprotective drugs. This review focuses on the importance of in silico manipulations of pyrazole and its derivatives for medicinal chemistry. The authors have discussed currently available information on the use of computational techniques like molecular docking, structure-based virtual screening (SBVS), molecular dynamics (MD) simulations, quantitative structure activity relationship (QSAR), comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) to drug design using pyrazole moieties. Pyrazole based drug design is mainly dependent on the integration of experimental and computational approaches. The authors feel that more studies need to be done to fully explore the pharmacological potential of the pyrazole moiety and in silico method can be of great help.
Collapse
Affiliation(s)
- Smriti Sharma
- Department of Chemistry, Miranda House, University of Delhi, India
| | - Vinayak Bhatia
- ICARE Eye Hospital and Postgraduate Institute, U.P., Noida, India
| |
Collapse
|
19
|
Wang Y, Zhao Y, Wei C, Tian N, Yan H. 4D-QSAR Molecular Modeling and Analysis of Flavonoid Derivatives as Acetylcholinesterase Inhibitors. Biol Pharm Bull 2021; 44:999-1006. [PMID: 34193695 DOI: 10.1248/bpb.b21-00265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Flavonoids are potential strikingly natural compounds with antioxidant activity and acetylcholinesterase (AChE) inhibitory activity for treating Alzheimer's disease (AD). In present study, in line with our interests in flavonoid derivatives as AChE inhibitors, a four-dimensional quantitative structure-activity relationship (4D-QSAR) molecular model was proposed. The data required to perform 4D-QSAR analysis includes 52 compounds reported in the literature, usually analogs, and their measured biological activities in a common assay. The model was generated by a complete set of 4D-QSAR program which was written by our group. The best model was found after trying multiple experiments. It had a good predictive ability with the cross-validation correlation coefficient Q2 = 0.77, the internal validation correlation coefficient R2 = 0.954, and the external validation correlation coefficient R2pred = 0.715. The molecular docking analysis was also carried out to understand exceedingly the interactions between flavonoids and the AChE targets, which was in good agreement with the 4D-QSAR model. Based on the information provided by the 4D-QSAR model and molecular docking analysis, the idea for optimizing the structures of flavonoids as AChE inhibitors was put forward which maybe provide theoretical guidance for the research and development of new AChE inhibitors.
Collapse
Affiliation(s)
- Yanyu Wang
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology
| | | | - Chaochun Wei
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology
| | - Nana Tian
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology.,Beijing Tide Pharmaceutical Co., Ltd
| | - Hong Yan
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology
| |
Collapse
|
20
|
Temml V, Kutil Z. Structure-based molecular modeling in SAR analysis and lead optimization. Comput Struct Biotechnol J 2021; 19:1431-1444. [PMID: 33777339 PMCID: PMC7979990 DOI: 10.1016/j.csbj.2021.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
In silico methods like molecular docking and pharmacophore modeling are established strategies in lead identification. Their successful application for finding new active molecules for a target is reported by a plethora of studies. However, once a potential lead is identified, lead optimization, with the focus on improving potency, selectivity, or pharmacokinetic parameters of a parent compound, is a much more complex task. Even though in silico molecular modeling methods could contribute a lot of time and cost-saving by rationally filtering synthetic optimization options, they are employed less widely in this stage of research. In this review, we highlight studies that have successfully used computer-aided SAR analysis in lead optimization and want to showcase sound methodology and easily accessible in silico tools for this purpose.
Collapse
Affiliation(s)
- Veronika Temml
- Institute of Pharmacy, Department of Pharmaceutical and Medicinal Chemistry, Paracelsus Medical University Salzburg, Strubergasse 21, 5020 Salzburg, Austria
| | - Zsofia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| |
Collapse
|
21
|
Bekono BD, Sona AN, Eni DB, Owono LCO, Megnassan E, Ntie-Kang F. Molecular mechanics approaches for rational drug design: forcefields and solvation models. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2019-0128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The use of molecular mechanics (MM) in understanding the energy and target of a drug, its structures, and properties has increased recently. This is achieved by the formulation of a simple MM energy equation, which represents the sum of the different energy interactions, often referred to as “forcefields” (FFs). The concept of FFs is now widely used as one of the fundamental tools for the in silico prediction of drug-target interactions. To generate more accurate predictions in the in silico drug discovery projects, the solvent effects are often taken into account. This review seeks to present an introductory guide for the reader on the fundamentals of MM with special emphasis on the role of FFs and the solvation models.
Collapse
Affiliation(s)
- Boris D. Bekono
- Department of Physics, Ecole Normale Supérieure , University of Yaoundé I , P.O. Box 47 , Yaoundé , Cameroon
| | - Alfred N. Sona
- Department of Chemistry , University of Buea , P.O. Box 63 , Buea , Cameroon
| | - Donatus B. Eni
- Department of Chemistry , University of Buea , P.O. Box 63 , Buea , Cameroon
- Department of Inorganic Chemistry, Faculty of Science , University of Yaoundé I , BP 812 , Yaoundé , Cameroon
| | - Luc C. O. Owono
- Department of Physics, Ecole Normale Supérieure , University of Yaoundé I , P.O. Box 47 , Yaoundé , Cameroon
- CEPAMOQ, Faculty of Science , University of Douala , P.O. Box 8580 , Douala , Cameroon
| | - Eugène Megnassan
- Laboratoire de Physique Fondamentale et Appliquée (LPFA) , University of Abobo-Adjamé (now Nangui Abrogoua) , Abidjan 02 , Côte d’Ivoire
| | - Fidele Ntie-Kang
- Department of Chemistry , University of Buea , P.O. Box 63 , Buea , Cameroon
- Department of Pharmaceutical Chemistry , Martin-Luther University Halle-Wittenberg , Kurt-Mothes Str. 4, 06120 Halle (Saale) , Germany
- Institut für Botanik , Technische Universität Dresden , Zellescher Weg 20b, 01062 Dresden , Germany
| |
Collapse
|
22
|
Hu ZH, Zhao TS, Liu HY, Lin QX, Tu GG, Yang BW. Synthesis and receptor dependent 4D-QSAR studies of 4,5-dihydro-1,3,4-oxadiazole derivatives targeting cannabinoid receptor. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:175-190. [PMID: 33618568 DOI: 10.1080/1062936x.2021.1879256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Cannabinoid receptor has been shown to be overexpressed in various types of cancers, especially non-small cell lung cancer. As a result, it could be used as novel target for anticancer treatments. Because receptor-dependent 4D-QSAR generates conformational ensemble profiles of compounds by molecular dynamics simulations at the binding site of the enzyme, this work describes the synthesis, biological activity evaluation and 4D-QSAR studies of 4,5-dihydro-1,3,4-oxadiazole derivatives targeting cannabinoid receptor. Compared with WIN55,212-2, compound 5 f showed the best antiproliferative activity. The receptor-dependent 4D-QSAR model was generated by multiple linear regression method using QSARINS. Leave-n-out cross-validation and chemical applicability domain were performed to analyse the independent test set and to verify the robustness of the model. The best 4D-QSAR model showed the following statistics: r2 = 0.8487, Q2LOO = 0.7667, Q2LNO = 0.7524, and r2Pred = 0.8358.
Collapse
Affiliation(s)
- Z H Hu
- Department of Medicinal Chemistry, School of Pharmaceutical Science, NanChang University, Nanchang, China
| | - T S Zhao
- Department of Medicinal Chemistry, School of Pharmaceutical Science, NanChang University, Nanchang, China
| | - H Y Liu
- Department of Traditional Chinese Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, China
| | - Q X Lin
- Department of Traditional Chinese Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, China
| | - G G Tu
- Department of Medicinal Chemistry, School of Pharmaceutical Science, NanChang University, Nanchang, China
| | - B W Yang
- Department of Medicinal Chemistry, School of Pharmaceutical Science, NanChang University, Nanchang, China
| |
Collapse
|
23
|
Hu Z, Lin Q, Liu H, Zhao T, Yang B, Tu G. Molecular dynamics-guided receptor-dependent 4D-QSAR studies of HDACs inhibitors. Mol Divers 2021; 26:757-768. [PMID: 33625673 DOI: 10.1007/s11030-021-10181-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/03/2021] [Indexed: 11/29/2022]
Abstract
Histone deacetylases (HDACs) were highlighted as a novel category of anticancer targets. Several HDACs inhibitors were approved for therapeutic use in cancer treatment. Comparatively, receptor-dependent 4D-QSAR, LQTA-QSAR, is a new approach which generates conformational ensemble profiles of compounds by molecular dynamics simulations at binding site of enzyme. This work describes a receptor-dependent 4D-QSAR studies on hydroxamate-based HDACs inhibitors. The 4D-QSAR model was generated by multiple linear regression method of QSARINS. Leave-N-out cross-validation (LNO) and Y-randomization were performed to analysis of the independent test set and to verify the robustness of the model. Best 4D-QSAR model showed the following statistics: R2 = 0.8117, Q2LOO = 0.6881, Q2LNO = 0.6830, R2Pred = 0.884. The results may be used for further virtual screening and design for novel HDACs inhibitors. The receptor dependent 4D-QSAR model was developed for the hydroxamate derivatives as HDAC inhibitors by making use of molecular dynamics simulation to obtain conformational ensemble profile for each compound. The multiple linear regression method was used to generate 4D-QSAR model with the suitable predictive ability and the excellent statistical parameters.
Collapse
Affiliation(s)
- Zhihao Hu
- Department of Medicinal Chemistry, School of Pharmaceutical Science, NanChang University, Nanchang, 330006, China
| | - Qianxia Lin
- Jiangxi University of Traditional Chinese Medicine, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Haiyun Liu
- Jiangxi University of Traditional Chinese Medicine, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Tiansheng Zhao
- Department of Medicinal Chemistry, School of Pharmaceutical Science, NanChang University, Nanchang, 330006, China
| | - Bowen Yang
- Department of Medicinal Chemistry, School of Pharmaceutical Science, NanChang University, Nanchang, 330006, China
| | - Guogang Tu
- Department of Medicinal Chemistry, School of Pharmaceutical Science, NanChang University, Nanchang, 330006, China.
| |
Collapse
|
24
|
Senior T, Botha MJ, Kennedy AR, Calvo-Castro J. Understanding the Contribution of Individual Amino Acid Residues in the Binding of Psychoactive Substances to Monoamine Transporters. ACS OMEGA 2020; 5:17223-17231. [PMID: 32715208 PMCID: PMC7376891 DOI: 10.1021/acsomega.0c01370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/19/2020] [Indexed: 05/05/2023]
Abstract
The development of point-of-care detection methodologies for biologically relevant analytes that can facilitate rapid and appropriate treatment is at the forefront of current research efforts and interests. Among the various approaches, those exploiting host-guest chemistries where the optoelectronic signals of the chemical sensor can be modulated upon interaction with the target analyte are of particular interest. In aiding their rational development, judicious selection of peripheral functional groups anchored to core motifs with desired properties is critical. Herein, we report an in-depth investigation of the binding of three psychoactive substances, MDAI, mexedrone, and phenibut, to receptors of the monoamine transporters for dopamine, norepinephrine, and serotonin, particularly focusing on the role of individual amino acid residues. We first evaluated the conformational flexibility of the ligands by comparing their experimentally determined crystal structure geometries to those optimized by means of quantum as well as molecular mechanics, observing significant changes in the case of phenibut. Molecular docking studies were employed to identify preferential binding sites by means of calculated docking scores. In all cases, irrespective of the monoamine transporter, psychoactive substances exhibited preferred interaction with the S1 or central site of the proteins, in line with previous studies. However, we observed that experimental trends for their relative potency on the three transporters were only reproduced in the case of mexedrone. Subsequently, to further understand these findings and to pave the way for the rational development of superior chemical sensors for these substances, we computed the individual contributions of each nearest neighbor amino acid residue to the binding to the target analytes. Interestingly, these results are now in agreement with those experimental potency trends. In addition, these observations were in all cases associated with key intermolecular interactions with neighboring residues, such as tyrosine and aspartic acid, in the binding of the ligands to the monoamine transporter for dopamine. As a result, we believe this work will be of interest to those engaged in the rational development of chemical sensors for small molecule analytes as well as to those interested in the use of computational approaches to further understand protein-ligand interactions.
Collapse
Affiliation(s)
- Tamara Senior
- School
of Life and Medical Sciences, University
of Hertfordshire, Hatfield AL10 9AB, U.K.
| | - Michelle J. Botha
- School
of Life and Medical Sciences, University
of Hertfordshire, Hatfield AL10 9AB, U.K.
| | - Alan R. Kennedy
- Department
of Pure & Applied Chemistry, University
of Strathclyde, Glasgow G1 1XL, U.K.
| | - Jesus Calvo-Castro
- School
of Life and Medical Sciences, University
of Hertfordshire, Hatfield AL10 9AB, U.K.
| |
Collapse
|
25
|
Schaller D, Wolber G. PyRod Enables Rational Homology Model-based Virtual Screening Against MCHR1. Mol Inform 2020; 39:e2000020. [PMID: 32329245 PMCID: PMC7317519 DOI: 10.1002/minf.202000020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/19/2020] [Indexed: 12/29/2022]
Abstract
Several encouraging pre-clinical results highlight the melanin-concentrating hormone receptor 1 (MCHR1) as promising target for anti-obesity drug development. Currently however, experimentally resolved structures of MCHR1 are not available, which complicates rational drug design campaigns. In this study, we aimed at developing accurate, homologymodel-based 3D pharmacophores against MCHR1. We show that traditional approaches involving docking of known active small molecules are hindered by the flexibility of binding pocket residues. Instead, we derived three-dimensional pharmacophores from molecular dynamics simulations by employing our novel open-source software PyRod. In a retrospective evaluation, the generated 3D pharmacophores were highly predictive returning up to 35 % of active molecules and showing an early enrichment (EF1) of up to 27.6. Furthermore, PyRod pharmacophores demonstrate higher sensitivity than ligand-based pharmacophores and deliver structural insights, which are key to rational lead optimization.
Collapse
Affiliation(s)
- David Schaller
- Pharmaceutical and Medicinal ChemistryFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Gerhard Wolber
- Pharmaceutical and Medicinal ChemistryFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| |
Collapse
|
26
|
Wang S, Witek J, Landrum GA, Riniker S. Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences. J Chem Inf Model 2020; 60:2044-2058. [PMID: 32155061 DOI: 10.1021/acs.jcim.0c00025] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The conformer generator ETKDG is a stochastic search method that utilizes distance geometry together with knowledge derived from experimental crystal structures. It has been shown to generate good conformers for acyclic, flexible molecules. This work builds on ETKDG to improve conformer generation of molecules containing small or large aliphatic (i.e., non-aromatic) rings. For one, we devise additional torsional-angle potentials to describe small aliphatic rings and adapt the previously developed potentials for acyclic bonds to facilitate the sampling of macrocycles. However, due to the larger number of degrees of freedom of macrocycles, the conformational space to sample is much broader than for small molecules, creating a challenge for conformer generators. We therefore introduce different heuristics to restrict the search space of macrocycles and bias the sampling toward more experimentally relevant structures. Specifically, we show the usage of elliptical geometry and customizable Coulombic interactions as heuristics. The performance of the improved ETKDG is demonstrated on test sets of diverse macrocycles and cyclic peptides. The code developed here will be incorporated into the 2020.03 release of the open-source cheminformatics library RDKit.
Collapse
Affiliation(s)
- Shuzhe Wang
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Jagna Witek
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | | | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| |
Collapse
|
27
|
Appavoo SD, Huh S, Diaz DB, Yudin AK. Conformational Control of Macrocycles by Remote Structural Modification. Chem Rev 2019; 119:9724-9752. [DOI: 10.1021/acs.chemrev.8b00742] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Solomon D. Appavoo
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
| | - Sungjoon Huh
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
| | - Diego B. Diaz
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
| | - Andrei K. Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
| |
Collapse
|
28
|
Ustach VD, Lakkaraju SK, Jo S, Yu W, Jiang W, MacKerell AD. Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. J Chem Inf Model 2019; 59:3018-3035. [PMID: 31034213 PMCID: PMC6597307 DOI: 10.1021/acs.jcim.9b00210] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chemical fragment cosolvent sampling techniques have become a versatile tool in ligand-protein binding prediction. Site-identification by ligand competitive saturation (SILCS) is one such method that maps the distribution of chemical fragments on a protein as free energy fields called FragMaps. Ligands are then simulated via Monte Carlo techniques in the field of the FragMaps (SILCS-MC) to predict their binding conformations and relative affinities for the target protein. Application of SILCS-MC using a number of different scoring schemes and MC sampling protocols against multiple protein targets was undertaken to evaluate and optimize the predictive capability of the method. Seven protein targets and 551 ligands with broad chemical variability were used to evaluate and optimize the model to maximize Pearson's correlation coefficient, Pearlman's predictive index, correct relative binding affinity, and root-mean-square error versus the absolute experimental binding affinities. Across the protein-ligand sets, the relative affinities of the ligands were predicted correctly an average of 69% of the time for the highest overall SILCS protocol. Training the FragMap weighting factors using a Bayesian machine learning (ML) algorithm led to an increase to an average 75% relative correct affinity predictions. Furthermore, once the optimal protocol is identified for a specific protein-ligand system average predictabilities of 76% are achieved. The ML algorithm is successful with small training sets of data (30 or more compounds) due to the use of physically correct FragMap weights as priors. Notably, the 76% correct relative prediction rate is similar to or better than free energy perturbation methods that are significantly computationally more expensive than SILCS. The results further support the utility of SILCS as a powerful and computationally accessible tool to support lead optimization and development in drug discovery.
Collapse
Affiliation(s)
- Vincent D. Ustach
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
| | | | - Sunhwan Jo
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, MD 21202
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
| | - Wenjuan Jiang
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
| | - Alexander D. MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, MD 21202
| |
Collapse
|
29
|
Ropp PJ, Spiegel JO, Walker JL, Green H, Morales GA, Milliken KA, Ringe JJ, Durrant JD. Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. J Cheminform 2019; 11:34. [PMID: 31127411 PMCID: PMC6534830 DOI: 10.1186/s13321-019-0358-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/15/2019] [Indexed: 12/20/2022] Open
Abstract
Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein–ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0.![]()
Collapse
Affiliation(s)
- Patrick J Ropp
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jacob O Spiegel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jennifer L Walker
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Harrison Green
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Guillermo A Morales
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA.,Innoventyx, LLC, Oro Valley, AZ, 85737, USA
| | - Katherine A Milliken
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - John J Ringe
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
| |
Collapse
|
30
|
4D-QSAR studies of CB2 cannabinoid receptor inverse agonists: a comparison to 3D-QSAR. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
31
|
Soulère L, Queneau Y. Conformational and docking studies of acyl homoserine lactones as a robust method to investigate bioactive conformations. Comput Biol Chem 2019; 79:48-54. [PMID: 30710805 DOI: 10.1016/j.compbiolchem.2019.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 11/16/2022]
Affiliation(s)
- Laurent Soulère
- Univ Lyon, Université Claude Bernard Lyon 1, INSA Lyon, CPE Lyon, UMR 5246, CNRS, ICBMS, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Bât. E. Lederer, 1 rue Victor Grignard, F-69622, Villeurbanne, France.
| | - Yves Queneau
- Univ Lyon, Université Claude Bernard Lyon 1, INSA Lyon, CPE Lyon, UMR 5246, CNRS, ICBMS, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Bât. E. Lederer, 1 rue Victor Grignard, F-69622, Villeurbanne, France
| |
Collapse
|
32
|
Abstract
Molecular dynamics (MD) simulations have been widely applied to computer-aided drug design (CADD). While MD has been used in a variety of applications such as free energy perturbation and long-time simulations, the accuracy of the results from those methods depends strongly on the force field used. Force fields for small molecules are crucial, as they not only serve as building blocks for developing force fields for larger biomolecules but also act as model compounds that will be transferred to ligands used in CADD. Currently, a wide range of small molecule force fields based on additive or nonpolarizable models have been developed. While these nonpolarizable force fields can produce reasonable estimations of physical properties and have shown success in a variety of systems, there is still room for improvements due to inherent limitations in these models including the lack of an electronic polarization response. For this reason, incorporating polarization effects into the energy function underlying a force field is believed to be an important step forward, giving rise to the development of polarizable force fields. Recent simulations of biological systems have indicated that polarizable force fields are able to provide a better physical representation of intermolecular interactions and, in many cases, better agreement with experimental properties than nonpolarizable, additive force fields. Therefore, this chapter focuses on the development of small molecule force fields with emphasis on polarizable models. It begins with a brief introduction on the importance of small molecule force fields and their evolution from additive to polarizable force fields. Emphasis is placed on the additive CHARMM General Force Field and the polarizable force field based on the classical Drude oscillator. The theory for the Drude polarizable force field and results for small molecules are presented showing their improvements over the additive model. The potential importance of polarization for their application in a wide range of biological systems including CADD is then discussed.
Collapse
Affiliation(s)
- Fang-Yu Lin
- Department of Pharmaceutical Sciences, Computer-Aided Drug Design Center, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, Computer-Aided Drug Design Center, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
| |
Collapse
|
33
|
Energy windows for computed compound conformers: covering artefacts or truly large reorganization energies? Future Med Chem 2019; 11:97-118. [DOI: 10.4155/fmc-2018-0400] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The generation of 3D conformers of small molecules underpins most computational drug discovery. Thus, the conformer quality is critical and depends on their energetics. A key parameter is the empirical conformational energy window (ΔEw), since only conformers within ΔEw are retained. However, ΔEw values in use appear unrealistically large. We analyze the factors pertaining to the conformer energetics and ΔEw. We argue that more attention must be focused on the problem of collapsed low-energy conformers. That is due to artificial intramolecular stabilization and occurs even with continuum solvation. Consequently, the conformational energy of extended bioactive structures is artefactually increased, which inflates ΔEw. Thus, this Perspective highlights the issues arising from low-energy conformers and suggests improvements via empirical or physics-based strategies.
Collapse
|
34
|
Simm GN, Vaucher AC, Reiher M. Exploration of Reaction Pathways and Chemical Transformation Networks. J Phys Chem A 2018; 123:385-399. [DOI: 10.1021/acs.jpca.8b10007] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Gregor N. Simm
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Alain C. Vaucher
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| |
Collapse
|
35
|
Gavane V, Koulgi S, Jani V, Uppuladinne MVN, Sonavane U, Joshi R. TANGO: A high through-put conformation generation and semiempirical method-based optimization tool for ligand molecules. J Comput Chem 2018; 40:900-909. [DOI: 10.1002/jcc.25706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/05/2018] [Accepted: 09/17/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Vivek Gavane
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing; Pune India
| | - Shruti Koulgi
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing; Pune India
| | - Vinod Jani
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing; Pune India
| | | | - Uddhavesh Sonavane
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing; Pune India
| | - Rajendra Joshi
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing; Pune India
| |
Collapse
|
36
|
Poli G, Seidel T, Langer T. Conformational Sampling of Small Molecules With iCon: Performance Assessment in Comparison With OMEGA. Front Chem 2018; 6:229. [PMID: 29971231 PMCID: PMC6018197 DOI: 10.3389/fchem.2018.00229] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/31/2018] [Indexed: 11/21/2022] Open
Abstract
Herein we present the algorithm and performance assessment of our newly developed conformer generator iCon that was implemented in LigandScout 4.0. Two data sets of high-quality X-ray structures of drug-like small molecules originating from the Protein Data Bank (200 ligands) and the Cambridge Structural Database (481 molecules) were used to validate iCon's performance in the reproduction of experimental conformations. OpenEye's conformer generator OMEGA was subjected to the same evaluation and served as a reference software in this analysis. We tested several setting patterns in order to identify the most suitable and efficient ones for conformational sampling with iCon; equivalent settings were also tested on OMEGA in order to compare the results obtained from the two programs and better assess iCon's performance. Overall, this study proved that iCon is able to generate reliable representative conformational ensembles of drug-like small molecules, yielding results comparable to those showed by OMEGA, and thus is ready to serve as a valuable tool for computer-aided drug design.
Collapse
Affiliation(s)
- Giulio Poli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Thomas Seidel
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Thierry Langer
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| |
Collapse
|
37
|
Sherman M, Contreras L. Computational approaches in design of nucleic acid-based therapeutics. Curr Opin Biotechnol 2018; 53:232-239. [PMID: 29562215 DOI: 10.1016/j.copbio.2017.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/29/2017] [Accepted: 12/01/2017] [Indexed: 12/17/2022]
Abstract
Recent advances in computational and experimental methods have led to novel avenues for therapeutic development. Utilization of nucleic acids as therapeutic agents and/or targets has been recently gaining attention due to their potential as high-affinity, selective molecular building blocks for various therapies. Notably, development of computational algorithms for predicting accessible RNA binding sites, identifying therapeutic target sequences, modeling delivery into tissues, and designing binding aptamers have enhanced therapeutic potential for this new drug category. Here, we review trends in drug development within the pharmaceutical industry and ways by which nucleic acid-based drugs have arisen as effective therapeutic candidates. In particular, we focus on computational and experimental approaches to nucleic acid-based drug design, commenting on challenges and outlooks for future applications.
Collapse
Affiliation(s)
- Mark Sherman
- Cell and Molecular Biology Graduate Program, University of Texas at Austin, 100 E. 24th Street, A6500, Austin, TX 78712, USA
| | - Lydia Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX 78712, USA.
| |
Collapse
|
38
|
Zhou LY, Peng JL, Wang JM, Geng YY, Zuo ZL, Hua Y. Structure-Activity Relationship of Xanthones as Inhibitors of Xanthine Oxidase. Molecules 2018; 23:molecules23020365. [PMID: 29425137 PMCID: PMC6017007 DOI: 10.3390/molecules23020365] [Citation(s) in RCA: 11] [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: 12/31/2017] [Revised: 02/03/2018] [Accepted: 02/07/2018] [Indexed: 12/03/2022] Open
Abstract
Polygala plants contain a large number of xanthones with good physiological activities. In our previous work, 18 xanthones were isolated from Polygala crotalarioides. Extented study of the chemical composition of the other species Polygala sibirica led to the separation of two new xanthones—3-hydroxy-1,2,6,7,8-pentamethoxy xanthone (A) and 6-O-β-d-glucopyranosyl-1,7-dimethoxy xanthone (C)—together with 14 known xanthones. Among them, some xanthones have a certain xanthine oxidase (XO) inhibitory activity. Furthemore, 14 xanthones as XO inhibitors were selected to develop three-dimensional quantitative structure–activity relationship (3D-QSAR) using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models. The CoMFA model predicted a q2 value of 0.613 and an r2 value of 0.997. The best CoMSIA model predicted a q2 value of 0.608 and an r2 value of 0.997 based on a combination of steric, electrostatic, and hydrophobic effects. The analysis of the contour maps from each model provided insight into the structural requirements for the development of more active XO inhibitors.
Collapse
Affiliation(s)
- Ling-Yun Zhou
- Key Laboratory for Forest Resources Conservation and Use in the Southwest Mountains of China (Southwest Forestry University), Ministry of Education, Kunming 650224, China.
- Anhui Provincial Engineering Research Center for Polysaccharide Drugs, School of Pharmacy, Wannan Medical College, Wuhu 241002, China.
| | - Jia-Le Peng
- State Key Laboratory of Phytochemistry and Plant Resource in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Jun-Ming Wang
- Key Laboratory for Forest Resources Conservation and Use in the Southwest Mountains of China (Southwest Forestry University), Ministry of Education, Kunming 650224, China.
| | - Yuan-Yuan Geng
- Key Laboratory for Forest Resources Conservation and Use in the Southwest Mountains of China (Southwest Forestry University), Ministry of Education, Kunming 650224, China.
| | - Zhi-Li Zuo
- State Key Laboratory of Phytochemistry and Plant Resource in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Yan Hua
- Key Laboratory for Forest Resources Conservation and Use in the Southwest Mountains of China (Southwest Forestry University), Ministry of Education, Kunming 650224, China.
| |
Collapse
|
39
|
Alihodžić S, Bukvić M, Elenkov IJ, Hutinec A, Koštrun S, Pešić D, Saxty G, Tomašković L, Žiher D. Current Trends in Macrocyclic Drug Discovery and beyond -Ro5. PROGRESS IN MEDICINAL CHEMISTRY 2018; 57:113-233. [DOI: 10.1016/bs.pmch.2018.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
40
|
Grimme S, Bannwarth C, Dohm S, Hansen A, Pisarek J, Pracht P, Seibert J, Neese F. Vollautomatisierte quantenchemische Berechnung von Spin-Spin- gekoppelten magnetischen Kernspinresonanzspektren. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708266] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry; Institut für Physikalische und Theoretische Chemie der Universität Bonn; Beringstraße 4 53115 Bonn Deutschland
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry; Institut für Physikalische und Theoretische Chemie der Universität Bonn; Beringstraße 4 53115 Bonn Deutschland
| | - Sebastian Dohm
- Mulliken Center for Theoretical Chemistry; Institut für Physikalische und Theoretische Chemie der Universität Bonn; Beringstraße 4 53115 Bonn Deutschland
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry; Institut für Physikalische und Theoretische Chemie der Universität Bonn; Beringstraße 4 53115 Bonn Deutschland
| | - Jana Pisarek
- Mulliken Center for Theoretical Chemistry; Institut für Physikalische und Theoretische Chemie der Universität Bonn; Beringstraße 4 53115 Bonn Deutschland
| | - Philipp Pracht
- Mulliken Center for Theoretical Chemistry; Institut für Physikalische und Theoretische Chemie der Universität Bonn; Beringstraße 4 53115 Bonn Deutschland
| | - Jakob Seibert
- Mulliken Center for Theoretical Chemistry; Institut für Physikalische und Theoretische Chemie der Universität Bonn; Beringstraße 4 53115 Bonn Deutschland
| | - Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion; Stiftstraße 32-34 45470 Mülheim an der Ruhr Deutschland
| |
Collapse
|
41
|
Grimme S, Bannwarth C, Dohm S, Hansen A, Pisarek J, Pracht P, Seibert J, Neese F. Fully Automated Quantum-Chemistry-Based Computation of Spin-Spin-Coupled Nuclear Magnetic Resonance Spectra. Angew Chem Int Ed Engl 2017; 56:14763-14769. [PMID: 28906074 PMCID: PMC5698732 DOI: 10.1002/anie.201708266] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Indexed: 11/27/2022]
Abstract
We present a composite procedure for the quantum‐chemical computation of spin–spin‐coupled 1H NMR spectra for general, flexible molecules in solution that is based on four main steps, namely conformer/rotamer ensemble (CRE) generation by the fast tight‐binding method GFN‐xTB and a newly developed search algorithm, computation of the relative free energies and NMR parameters, and solving the spin Hamiltonian. In this way the NMR‐specific nuclear permutation problem is solved, and the correct spin symmetries are obtained. Energies, shielding constants, and spin–spin couplings are computed at state‐of‐the‐art DFT levels with continuum solvation. A few (in)organic and transition‐metal complexes are presented, and very good, unprecedented agreement between the theoretical and experimental spectra was achieved. The approach is routinely applicable to systems with up to 100–150 atoms and may open new avenues for the detailed (conformational) structure elucidation of, for example, natural products or drug molecules.
Collapse
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstrasse 4, 53115, Bonn, Germany
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstrasse 4, 53115, Bonn, Germany
| | - Sebastian Dohm
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstrasse 4, 53115, Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstrasse 4, 53115, Bonn, Germany
| | - Jana Pisarek
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstrasse 4, 53115, Bonn, Germany
| | - Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstrasse 4, 53115, Bonn, Germany
| | - Jakob Seibert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstrasse 4, 53115, Bonn, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 32-34, 45470, Mülheim an der Ruhr, Germany
| |
Collapse
|
42
|
Sirci F, Napolitano F, Pisonero-Vaquero S, Carrella D, Medina DL, di Bernardo D. Comparing structural and transcriptional drug networks reveals signatures of drug activity and toxicity in transcriptional responses. NPJ Syst Biol Appl 2017; 3:23. [PMID: 28861278 PMCID: PMC5572457 DOI: 10.1038/s41540-017-0022-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/27/2017] [Accepted: 07/07/2017] [Indexed: 02/07/2023] Open
Abstract
We performed an integrated analysis of drug chemical structures and drug-induced transcriptional responses. We demonstrated that a network representing three-dimensional structural similarities among 5452 compounds can be used to automatically group together drugs with similar scaffolds, physicochemical parameters and mode-of-action. We compared the structural network to a network representing transcriptional similarities among a subset of 1309 drugs for which transcriptional response were available in the Connectivity Map data set. Analysis of structurally similar, but transcriptionally different drugs sharing the same MOA enabled us to detect and remove weak and noisy transcriptional responses, greatly enhancing the reliability of transcription-based approaches to drug discovery and drug repositioning. Cardiac glycosides exhibited the strongest transcriptional responses with a significant induction of pathways related to epigenetic regulation, which suggests an epigenetic mechanism of action for these drugs. Drug classes with the weakest transcriptional responses tended to induce expression of cytochrome P450 enzymes, hinting at drug-induced drug resistance. Analysis of transcriptionally similar, but structurally different drugs with unrelated MOA, led us to the identification of a 'toxic' transcriptional signature indicative of lysosomal stress (lysosomotropism) and lipid accumulation (phospholipidosis) partially masking the target-specific transcriptional effects of these drugs. We found that this transcriptional signature is shared by 258 compounds and it is associated to the activation of the transcription factor TFEB, a master regulator of lysosomal biogenesis and autophagy. Finally, we built a predictive Random Forest model of these 258 compounds based on 128 physicochemical parameters, which should help in the early identification of potentially toxic drug candidates. Transcriptional responses to drug treatment can reveal mechanism of action and off-target effects thus enabling drug repositioning, but only if measured in the appropriate cells at clinically relevant concentrations. A team led by Diego di Bernardo and Diego Medina generated a network representing structural similarities among compounds to automatically group together drugs with similar scaffolds and MOA. By comparing the structural drug network with a transcriptional drug network based on similarities in transcriptional response, the team observed broad differences between the two. This observation led to the identification of a transcriptional signature related lysosomal stress and phospholipidosis, and a physicochemical model to identify such compounds. These results provide general guidelines to prevent erroneous conclusion when using transcriptional responses of small molecules for drug discovery and drug repositioning
Collapse
Affiliation(s)
- Francesco Sirci
- Telethon Institute of Genetics and Medicine (TIGEM), System Biology and Bioinformatics lab. and High Content Screening facility, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Francesco Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM), System Biology and Bioinformatics lab. and High Content Screening facility, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Sandra Pisonero-Vaquero
- Telethon Institute of Genetics and Medicine (TIGEM), System Biology and Bioinformatics lab. and High Content Screening facility, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Diego Carrella
- Telethon Institute of Genetics and Medicine (TIGEM), System Biology and Bioinformatics lab. and High Content Screening facility, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Diego L Medina
- Telethon Institute of Genetics and Medicine (TIGEM), System Biology and Bioinformatics lab. and High Content Screening facility, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), System Biology and Bioinformatics lab. and High Content Screening facility, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy.,Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy
| |
Collapse
|
43
|
Abstract
The generation of conformations for small molecules is a problem of continuing interest in cheminformatics and computational drug discovery. This review will present an overview of methods used to sample conformational space, focusing on those methods designed for organic molecules commonly of interest in drug discovery. Different approaches to both the sampling of conformational space and the scoring of conformational stability will be compared and contrasted, with an emphasis on those methods suitable for conformer sampling of large numbers of drug-like molecules. Particular attention will be devoted to the appropriate utilization of information from experimental solid-state structures in validating and evaluating the performance of these tools. The review will conclude with some areas worthy of further investigation.
Collapse
Affiliation(s)
- Paul C D Hawkins
- OpenEye Scientific , 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States
| |
Collapse
|
44
|
Kim H, Jang C, Yadav DK, Kim MH. The comparison of automated clustering algorithms for resampling representative conformer ensembles with RMSD matrix. J Cheminform 2017; 9:21. [PMID: 29086188 PMCID: PMC5364127 DOI: 10.1186/s13321-017-0208-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/15/2017] [Indexed: 12/01/2022] Open
Abstract
Background The accuracy of any 3D-QSAR, Pharmacophore and 3D-similarity based chemometric target fishing models are highly dependent on a reasonable sample of active conformations. Since a number of diverse conformational sampling algorithm exist, which exhaustively generate enough conformers, however model building methods relies on explicit number of common conformers. Results In this work, we have attempted to make clustering algorithms, which could find reasonable number of representative conformer ensembles automatically with asymmetric dissimilarity matrix generated from openeye tool kit. RMSD was the important descriptor (variable) of each column of the N × N matrix considered as N variables describing the relationship (network) between the conformer (in a row) and the other N conformers. This approach used to evaluate the performance of the well-known clustering algorithms by comparison in terms of generating representative conformer ensembles and test them over different matrix transformation functions considering the stability. In the network, the representative conformer group could be resampled for four kinds of algorithms with implicit parameters. The directed dissimilarity matrix becomes the only input to the clustering algorithms. Conclusions Dunn index, Davies–Bouldin index, Eta-squared values and omega-squared values were used to evaluate the clustering algorithms with respect to the compactness and the explanatory power. The evaluation includes the reduction (abstraction) rate of the data, correlation between the sizes of the population and the samples, the computational complexity and the memory usage as well. Every algorithm could find representative conformers automatically without any user intervention, and they reduced the data to 14–19% of the original values within 1.13 s per sample at the most. The clustering methods are simple and practical as they are fast and do not ask for any explicit parameters. RCDTC presented the maximum Dunn and omega-squared values of the four algorithms in addition to consistent reduction rate between the population size and the sample size. The performance of the clustering algorithms was consistent over different transformation functions. Moreover, the clustering method can also be applied to molecular dynamics sampling simulation results. Electronic supplementary material The online version of this article (doi:10.1186/s13321-017-0208-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hyoungrae Kim
- Department of Data Management, KEIS, 56 Mullae-ro 20-gil, Yeongdeungpo-gu, Seoul, Republic of Korea.
| | - Cheongyun Jang
- Department of Pharmacy, College of Pharmacy, Yeonsu-gu, Incheon, Republic of Korea
| | - Dharmendra K Yadav
- Department of Pharmacy, College of Pharmacy, Yeonsu-gu, Incheon, Republic of Korea
| | - Mi-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Yeonsu-gu, Incheon, Republic of Korea. .,Gachon Institute of Pharmaceutical Science, Gachon University, Yeonsu-gu, Incheon, Republic of Korea.
| |
Collapse
|
45
|
Abstract
Computational approaches are useful tools to interpret and guide experiments to expedite the antibiotic drug design process. Structure-based drug design (SBDD) and ligand-based drug design (LBDD) are the two general types of computer-aided drug design (CADD) approaches in existence. SBDD methods analyze macromolecular target 3-dimensional structural information, typically of proteins or RNA, to identify key sites and interactions that are important for their respective biological functions. Such information can then be utilized to design antibiotic drugs that can compete with essential interactions involving the target and thus interrupt the biological pathways essential for survival of the microorganism(s). LBDD methods focus on known antibiotic ligands for a target to establish a relationship between their physiochemical properties and antibiotic activities, referred to as a structure-activity relationship (SAR), information that can be used for optimization of known drugs or guide the design of new drugs with improved activity. In this chapter, standard CADD protocols for both SBDD and LBDD will be presented with a special focus on methodologies and targets routinely studied in our laboratory for antibiotic drug discoveries.
Collapse
|
46
|
Wang Q, Sciabola S, Barreiro G, Hou X, Bai G, Shapiro MJ, Koehn F, Villalobos A, Jacobson MP. Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction. J Chem Inf Model 2016; 56:2194-2206. [PMID: 27731994 DOI: 10.1021/acs.jcim.6b00237] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Macrocycles pose challenges for computer-aided drug design due to their conformational complexity. One fundamental challenge is identifying all low-energy conformations of the macrocyclic ring, which is important for modeling target binding, passive membrane permeation, and other conformation-dependent properties. Macrocyclic polyketides are medically and biologically important natural products characterized by structural and functional diversity. Advances in synthetic biology and semisynthetic methods may enable creation of an even more diverse set of non-natural product polyketides for drug discovery and other applications. However, the conformational sampling of these flexible compounds remains demanding. We developed and optimized a dihedral angle-based macrocycle conformational sampling method for macrocycles of arbitrary structure, and here we apply it to diverse polyketide natural products. First, we evaluated its performance using a data set of 37 polyketides with available crystal structures, with 9-22 rotatable bonds in the macrocyclic ring. Our optimized protocol was able to reproduce the crystal structure of polyketides' aglycone backbone within 0.50 Å RMSD for 31 out of 37 polyketides. Consistent with prior structural studies, our analysis suggests that polyketides tend to have multiple distinct low-energy structures, including the bioactive (target-bound) conformation as well as others of unknown significance. For this reason, we also introduce a strategy to improve both efficiency and accuracy of the conformational search by utilizing torsional restraints derived from NMR vicinal proton couplings to restrict the conformational search. Finally, as a first application of the method, we made blinded predictions of the passive membrane permeability of a diverse set of polyketides, based on their predicted structures in low- and high-dielectric media.
Collapse
Affiliation(s)
- Qin Wang
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| | - Simone Sciabola
- Neuroscience and Pain Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Gabriela Barreiro
- Neuroscience and Pain Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Xinjun Hou
- Neuroscience and Pain Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | | | | | | | - Anabella Villalobos
- Neuroscience and Pain Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| |
Collapse
|
47
|
Foloppe N, Chen IJ. Towards understanding the unbound state of drug compounds: Implications for the intramolecular reorganization energy upon binding. Bioorg Med Chem 2016; 24:2159-89. [PMID: 27061672 DOI: 10.1016/j.bmc.2016.03.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/09/2016] [Accepted: 03/12/2016] [Indexed: 01/24/2023]
Abstract
There has been an explosion of structural information for pharmaceutical compounds bound to biological targets, but the conformations and dynamics of compounds free in solution are poorly characterized, if at all. Yet, knowledge of the unbound state is essential to understand the fundamentals of molecular recognition, including the much debated conformational intramolecular reorganization energy of a compound upon binding (ΔEReorg). Also, dependable observation of the unbound compounds is important for ligand-based drug discovery, e.g. with pharmacophore modelling. Here, these questions are addressed with long (⩾0.5μs) state-of-the-art molecular dynamics (MD) simulations of 26 compounds (including 7 approved drugs) unbound in explicit solvent. These compounds were selected to be chemically diverse, with a range of flexibility, and good quality bioactive X-ray structures. The MD-simulated free compounds are compared to their bioactive structure and conformers generated with ad hoc sampling in vacuo or with implicit generalized Born (GB) aqueous solvation models. The GB conformational models clearly depart from those obtained in explicit solvent, and suffer from conformational collapse almost as severe as in vacuo. Thus, the global energy minima in vacuo or with GB are not suitable representations of the unbound state, which can instead be extensively sampled by MD simulations. Many, but not all, MD-simulated compounds displayed some structural similarity to their bioactive structure, supporting the notion of conformational pre-organization for binding. The ligand-protein complexes were also simulated in explicit solvent, to estimate ΔEReorg as an enthalpic difference ΔHReorg between the intramolecular energies in the bound and unbound states. This fresh approach yielded ΔHReorg values⩽6kcal/mol for 18 out of 26 compounds. For three particularly polar compounds 15⩽ΔHReorg⩽20kcal/mol, supporting the notion that ΔHReorg can be substantial. Those large ΔHReorg values correspond to a redistribution of electrostatic interactions upon binding. Overall, the study illustrates how MD simulations offer a promising avenue to characterize the unbound state of medicinal compounds.
Collapse
Affiliation(s)
- Nicolas Foloppe
- Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB21 6GB, UK.
| | - I-Jen Chen
- Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB21 6GB, UK.
| |
Collapse
|
48
|
Shar PA, Tao W, Gao S, Huang C, Li B, Zhang W, Shahen M, Zheng C, Bai Y, Wang Y. Pred-binding: large-scale protein-ligand binding affinity prediction. J Enzyme Inhib Med Chem 2016; 31:1443-50. [PMID: 26888050 DOI: 10.3109/14756366.2016.1144594] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Drug target interactions (DTIs) are crucial in pharmacology and drug discovery. Presently, experimental determination of compound-protein interactions remains challenging because of funding investment and difficulties of purifying proteins. In this study, we proposed two in silico models based on support vector machine (SVM) and random forest (RF), using 1589 molecular descriptors and 1080 protein descriptors in 9948 ligand-protein pairs to predict DTIs that were quantified by Ki values. The cross-validation coefficient of determination of 0.6079 for SVM and 0.6267 for RF were obtained, respectively. In addition, the two-dimensional (2D) autocorrelation, topological charge indices and three-dimensional (3D)-MoRSE descriptors of compounds, the autocorrelation descriptors and the amphiphilic pseudo-amino acid composition of protein are found most important for Ki predictions. These models provide a new opportunity for the prediction of ligand-receptor interactions that will facilitate the target discovery and toxicity evaluation in drug development.
Collapse
Affiliation(s)
- Piar Ali Shar
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Weiyang Tao
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Shuo Gao
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Chao Huang
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Bohui Li
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Wenjuan Zhang
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Mohamed Shahen
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Chunli Zheng
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Yaofei Bai
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Yonghua Wang
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| |
Collapse
|
49
|
Kothiwale S, Mendenhall JL, Meiler J. BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library. J Cheminform 2015; 7:47. [PMID: 26473018 PMCID: PMC4607025 DOI: 10.1186/s13321-015-0095-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/03/2015] [Indexed: 12/14/2022] Open
Abstract
The interaction of a small molecule with a protein target depends on its ability to adopt a three-dimensional structure that is complementary. Therefore, complete and rapid prediction of the conformational space a small molecule can sample is critical for both structure- and ligand-based drug discovery algorithms such as small molecule docking or three-dimensional quantitative structure–activity relationships. Here we have derived a database of small molecule fragments frequently sampled in experimental structures within the Cambridge Structure Database and the Protein Data Bank. Likely conformations of these fragments are stored as ‘rotamers’ in analogy to amino acid side chain rotamer libraries used for rapid sampling of protein conformational space. Explicit fragments take into account correlations between multiple torsion bonds and effect of substituents on torsional profiles. A conformational ensemble for small molecules can then be generated by recombining fragment rotamers with a Monte Carlo search strategy. BCL::Conf was benchmarked against other conformer generator methods including Confgen, Moe, Omega and RDKit in its ability to recover experimentally determined protein bound conformations of small molecules, diversity of conformational ensembles, and sampling rate. BCL::Conf recovers at least one conformation with a root mean square deviation of 2 Å or better to the experimental structure for 99 % of the small molecules in the Vernalis benchmark dataset. The ‘rotamer’ approach will allow integration of BCL::Conf into respective computational biology programs such as Rosetta.Conformation sampling is carried out using explicit fragment conformations derived from crystallographic structure databases. Molecules from the database are decomposed into fragments and most likely conformations/rotamers are used to sample correspondng sub-structure of a molecule of interest. ![]()
Collapse
Affiliation(s)
- Sandeepkumar Kothiwale
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232 USA
| | - Jeffrey L Mendenhall
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232 USA
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232 USA ; Department of Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, TN 37212 USA
| |
Collapse
|
50
|
Engel J, Richters A, Getlik M, Tomassi S, Keul M, Termathe M, Lategahn J, Becker C, Mayer-Wrangowski S, Grütter C, Uhlenbrock N, Krüll J, Schaumann N, Eppmann S, Kibies P, Hoffgaard F, Heil J, Menninger S, Ortiz-Cuaran S, Heuckmann JM, Tinnefeld V, Zahedi RP, Sos ML, Schultz-Fademrecht C, Thomas RK, Kast SM, Rauh D. Targeting Drug Resistance in EGFR with Covalent Inhibitors: A Structure-Based Design Approach. J Med Chem 2015; 58:6844-63. [PMID: 26275028 DOI: 10.1021/acs.jmedchem.5b01082] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Receptor tyrosine kinases represent one of the prime targets in cancer therapy, as the dysregulation of these elementary transducers of extracellular signals, like the epidermal growth factor receptor (EGFR), contributes to the onset of cancer, such as non-small cell lung cancer (NSCLC). Strong efforts were directed to the development of irreversible inhibitors and led to compound CO-1686, which takes advantage of increased residence time at EGFR by alkylating Cys797 and thereby preventing toxic effects. Here, we present a structure-based approach, rationalized by subsequent computational analysis of conformational ligand ensembles in solution, to design novel and irreversible EGFR inhibitors based on a screening hit that was identified in a phenotype screen of 80 NSCLC cell lines against approximately 1500 compounds. Using protein X-ray crystallography, we deciphered the binding mode in engineered cSrc (T338M/S345C), a validated model system for EGFR-T790M, which constituted the basis for further rational design approaches. Chemical synthesis led to further compound collections that revealed increased biochemical potency and, in part, selectivity toward mutated (L858R and L858R/T790M) vs nonmutated EGFR. Further cell-based and kinetic studies were performed to substantiate our initial findings. Utilizing proteolytic digestion and nano-LC-MS/MS analysis, we confirmed the alkylation of Cys797.
Collapse
Affiliation(s)
- Julian Engel
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - André Richters
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Matthäus Getlik
- Chemical Genomics Centre of the Max-Planck Society , Otto-Hahn-Straße 15, D-44227 Dortmund, Germany
| | - Stefano Tomassi
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Marina Keul
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Martin Termathe
- Chemical Genomics Centre of the Max-Planck Society , Otto-Hahn-Straße 15, D-44227 Dortmund, Germany
| | - Jonas Lategahn
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Christian Becker
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Svenja Mayer-Wrangowski
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Christian Grütter
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Niklas Uhlenbrock
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Jasmin Krüll
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Niklas Schaumann
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Simone Eppmann
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Patrick Kibies
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Franziska Hoffgaard
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Jochen Heil
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Sascha Menninger
- Lead Discovery Center GmbH , Otto-Hahn-Straße 15, D-44227 Dortmund, Germany
| | - Sandra Ortiz-Cuaran
- Department of Translational Genomics, Medical Faculty, University of Cologne , Weyertal 115b, D-50931 Cologne, Germany
| | - Johannes M Heuckmann
- Department of Translational Genomics, Medical Faculty, University of Cologne , Weyertal 115b, D-50931 Cologne, Germany
| | - Verena Tinnefeld
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , D-44139 Dortmund, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , D-44139 Dortmund, Germany
| | - Martin L Sos
- Department of Translational Genomics, Medical Faculty, University of Cologne , Weyertal 115b, D-50931 Cologne, Germany.,Molecular Pathology, University Hospital of Cologne , Kerpenerstraße 62, D-50937 Cologne, Germany
| | | | - Roman K Thomas
- Department of Translational Genomics, Medical Faculty, University of Cologne , Weyertal 115b, D-50931 Cologne, Germany.,Department of Pathology, University of Cologne , Joseph-Stelzmann Straße 9, D-50931 Cologne, Germany
| | - Stefan M Kast
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany
| | - Daniel Rauh
- Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany.,Chemical Genomics Centre of the Max-Planck Society , Otto-Hahn-Straße 15, D-44227 Dortmund, Germany
| |
Collapse
|