1
|
Arora P, Behera M, Saraf SA, Shukla R. Leveraging Artificial Intelligence for Synergies in Drug Discovery: From Computers to Clinics. Curr Pharm Des 2024; 30:2187-2205. [PMID: 38874046 DOI: 10.2174/0113816128308066240529121148] [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: 02/01/2024] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 06/15/2024]
Abstract
Over the period of the preceding decade, artificial intelligence (AI) has proved an outstanding performance in entire dimensions of science including pharmaceutical sciences. AI uses the concept of machine learning (ML), deep learning (DL), and neural networks (NNs) approaches for novel algorithm and hypothesis development by training the machines in multiple ways. AI-based drug development from molecule identification to clinical approval tremendously reduces the cost of development and the time over conventional methods. The COVID-19 vaccine development and approval by regulatory agencies within 1-2 years is the finest example of drug development. Hence, AI is fast becoming a boon for scientific researchers to streamline their advanced discoveries. AI-based FDA-approved nanomedicines perform well as target selective, synergistic therapies, recolonize the theragnostic pharmaceutical stream, and significantly improve drug research outcomes. This comprehensive review delves into the fundamental aspects of AI along with its applications in the realm of pharmaceutical life sciences. It explores AI's role in crucial areas such as drug designing, drug discovery and development, traditional Chinese medicine, integration of multi-omics data, as well as investigations into drug repurposing and polypharmacology studies.
Collapse
Affiliation(s)
- Priyanka Arora
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, Near CRPF Base Camp, Bijnor-Sisendi Road, Sarojini Nagar, Lucknow (UP)-226002, India
| | - Manaswini Behera
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, Near CRPF Base Camp, Bijnor-Sisendi Road, Sarojini Nagar, Lucknow (UP)-226002, India
| | - Shubhini A Saraf
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, Near CRPF Base Camp, Bijnor-Sisendi Road, Sarojini Nagar, Lucknow (UP)-226002, India
| | - Rahul Shukla
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, Near CRPF Base Camp, Bijnor-Sisendi Road, Sarojini Nagar, Lucknow (UP)-226002, India
| |
Collapse
|
2
|
Stillson NJ, Anderson KE, Reich NO. In silico study of selective inhibition mechanism of S-adenosyl-L-methionine analogs for human DNA methyltransferase 3A. Comput Biol Chem 2023; 102:107796. [PMID: 36495748 DOI: 10.1016/j.compbiolchem.2022.107796] [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: 07/08/2022] [Revised: 11/19/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022]
Abstract
Epigenetic mechanisms leading to transcriptional regulation, including DNA methylation, are frequently dysregulated in diverse cancers. Interfering with aberrant DNA methylation performed by DNA cytosine methyltransferases (DNMTs) is a clinically validated approach. In particular, the selective inhibition of the de novo DNMT3A and DNMT3B enzymes, whose expression is limited to early embryogenesis, adult stem cells, and in cancers, is particularly attractive; such selectivity is likely to attenuate the dose limiting toxicity shown by current, non-selective DNMT inhibitors. We use molecular dynamics (MD) based computational analysis to study known small molecule binders of DNMT3A, then propose reversible, tight binding, and selective inhibitors that exploit the Asn1192/Arg688 difference between the maintenance DNMT1 and DNMT3A near the active site. A similar strategy exploiting the presence of a unique active site cysteine Cys666 is used to propose DNMT3A-selective irreversible inhibitors. We report our results of relative binding energies of the known and proposed compounds estimated using MM/GBSA and umbrella sampling (US) techniques, and our evaluation of other end-point binding free energy calculation methods for these receptors. These calculations offer insight into the potential for small molecules to selectively target the active site of DNMT3A.
Collapse
Affiliation(s)
- Nathaniel J Stillson
- The Department of Chemistry and Biochemistry University of California, Santa Barbara 93106-9510, USA
| | - Kyle E Anderson
- The Department of Chemistry and Biochemistry University of California, Santa Barbara 93106-9510, USA
| | - Norbert O Reich
- The Department of Chemistry and Biochemistry University of California, Santa Barbara 93106-9510, USA.
| |
Collapse
|
3
|
Řezáč J, Stewart JJP. How well do semiempirical QM methods describe the structure of proteins? J Chem Phys 2023; 158:044118. [PMID: 36725526 DOI: 10.1063/5.0135091] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Semiempirical quantum-mechanical (QM) computational methods are an increasingly popular tool for the study of biomolecular systems. They were, however, developed and tested mostly on small model molecules. In this work, we explore one topic fundamental to these applications: the ability of the methods to describe the structure of proteins. In a set of 19 proteins for which a crystal structure with very high resolution is available, we analyze the properties of the protein geometries optimized using several semiempirical QM methods including PM6-D3H4, PM7, and GFN2-xTB. Some of the methods provide a very good description of the general structural features of the protein, yielding results better than or comparable to the AMBER ff03 force field. However, PM7 and PM6-D3H4 optimizations introduce artificial close contacts in the structure, which is partially remediated by reparameterization.
Collapse
Affiliation(s)
- J Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16000 Prague, Czech Republic
| | - J J P Stewart
- Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, Colorado 80921, USA
| |
Collapse
|
4
|
Dutkiewicz Z. Computational methods for calculation of protein-ligand binding affinities in structure-based drug design. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2020-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Abstract
Drug design is an expensive and time-consuming process. Any method that allows reducing the time the costs of the drug development project can have great practical value for the pharmaceutical industry. In structure-based drug design, affinity prediction methods are of great importance. The majority of methods used to predict binding free energy in protein-ligand complexes use molecular mechanics methods. However, many limitations of these methods in describing interactions exist. An attempt to go beyond these limits is the application of quantum-mechanical description for all or only part of the analyzed system. However, the extensive use of quantum mechanical (QM) approaches in drug discovery is still a demanding challenge. This chapter briefly reviews selected methods used to calculate protein-ligand binding affinity applied in virtual screening (VS), rescoring of docked poses, and lead optimization stage, including QM methods based on molecular simulations.
Collapse
Affiliation(s)
- Zbigniew Dutkiewicz
- Department of Chemical Technology of Drugs , Poznan University of Medical Sciences , ul. Grunwaldzka 6 , 60-780 Poznań , Poznan , 60-780, Poland
| |
Collapse
|
5
|
Wang H, Liu H, Ning S, Zeng C, Zhao Y. DLSSAffinity: protein-ligand binding affinity prediction via a deep learning model. Phys Chem Chem Phys 2022; 24:10124-10133. [PMID: 35416807 DOI: 10.1039/d1cp05558e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Evaluating the protein-ligand binding affinity is a substantial part of the computer-aided drug discovery process. Most of the proposed computational methods predict protein-ligand binding affinity using either limited full-length protein 3D structures or simple full-length protein sequences as the input features. Thus, protein-ligand binding affinity prediction remains a fundamental challenge in drug discovery. In this study, we proposed a novel deep learning-based approach, DLSSAffinity, to accurately predict the protein-ligand binding affinity. Unlike the existing methods, DLSSAffinity uses the pocket-ligand structural pairs as the local information to predict short-range direct interactions. Besides, DLSSAffinity also uses the full-length protein sequence and ligand SMILES as the global information to predict long-range indirect interactions. We tested DLSSAffinity on the PDBbind benchmark. The results showed that DLSSAffinity achieves Pearson's R = 0.79, RMSE = 1.40, and SD = 1.35 on the test set. Comparing DLSSAffinity with the existing state-of-the-art deep learning-based binding affinity prediction methods, the DLSSAffinity model outperforms other models. These results demonstrate that combining global sequence and local structure information as the input features of a deep learning model can improve the accuracy of protein-ligand binding affinity prediction.
Collapse
Affiliation(s)
- Huiwen Wang
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, China.
| | - Haoquan Liu
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China.
| | - Shangbo Ning
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China.
| | - Chengwei Zeng
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China.
| | - Yunjie Zhao
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China.
| |
Collapse
|
6
|
López R, Díaz N, Francisco E, Martín-Pendás A, Suárez D. QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach. J Chem Inf Model 2022; 62:1510-1524. [PMID: 35212531 PMCID: PMC8965874 DOI: 10.1021/acs.jcim.1c01372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interacting quantum atoms (IQA) method decomposes the quantum mechanical (QM) energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. Here, we demonstrate that IQA, enhanced with molecular mechanics (MM) and Poisson-Boltzmann surface-area (PBSA) solvation methods, is naturally extended to the realm of hybrid QM/MM methodologies, yielding intra- and inter-residue energy terms that characterize all kinds of covalent and noncovalent bonding interactions. To test the robustness of this approach, both metal-water interactions and QM/MM boundary artifacts are characterized in terms of the IQA descriptors derived from QM regions of varying size in Zn(II)- and Mg(II)-water clusters. In addition, we analyze a homologous series of inhibitors in complex with a matrix metalloproteinase (MMP-12) by carrying out QM/MM-PBSA calculations on their crystallographic structures followed by IQA energy decomposition. Overall, these applications not only show the advantages of the IQA QM/MM approach but also address some of the challenges lying ahead for expanding the QM/MM methodology.
Collapse
Affiliation(s)
- Roberto López
- Departamento de Química y Física Aplicadas, Universidad de León, Facultad de Biología, Campus de Vegazana s/n, 24071 León (Castilla y León), Spain
| | - Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Angel Martín-Pendás
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| |
Collapse
|
7
|
Abstract
Abstract
Machine learning (ML) has revolutionised the field of structure-based drug design (SBDD) in recent years. During the training stage, ML techniques typically analyse large amounts of experimentally determined data to create predictive models in order to inform the drug discovery process. Deep learning (DL) is a subfield of ML, that relies on multiple layers of a neural network to extract significantly more complex patterns from experimental data, and has recently become a popular choice in SBDD. This review provides a thorough summary of the recent DL trends in SBDD with a particular focus on de novo drug design, binding site prediction, and binding affinity prediction of small molecules.
Collapse
|
8
|
Spinello A, Borišek J, Pavlin M, Janoš P, Magistrato A. Computing Metal-Binding Proteins for Therapeutic Benefit. ChemMedChem 2021; 16:2034-2049. [PMID: 33740297 DOI: 10.1002/cmdc.202100109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Indexed: 01/18/2023]
Abstract
Over one third of biomolecules rely on metal ions to exert their cellular functions. Metal ions can play a structural role by stabilizing the structure of biomolecules, a functional role by promoting a wide variety of biochemical reactions, and a regulatory role by acting as messengers upon binding to proteins regulating cellular metal-homeostasis. These diverse roles in biology ascribe critical implications to metal-binding proteins in the onset of many diseases. Hence, it is of utmost importance to exhaustively unlock the different mechanistic facets of metal-binding proteins and to harness this knowledge to rationally devise novel therapeutic strategies to prevent or cure pathological states associated with metal-dependent cellular dysfunctions. In this compendium, we illustrate how the use of a computational arsenal based on docking, classical, and quantum-classical molecular dynamics simulations can contribute to extricate the minutiae of the catalytic, transport, and inhibition mechanisms of metal-binding proteins at the atomic level. This knowledge represents a fertile ground and an essential prerequisite for selectively targeting metal-binding proteins with small-molecule inhibitors aiming to (i) abrogate deregulated metal-dependent (mis)functions or (ii) leverage metal-dyshomeostasis to selectively trigger harmful cells death.
Collapse
Affiliation(s)
- Angelo Spinello
- National Research Council of Italy (CNR)-, Institute of Materials (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy
| | - Jure Borišek
- National Institute of Chemistry Institution Hajdrihova ulica 19, 1000, Ljubljana, Slovenia
| | - Matic Pavlin
- Laboratory of Microsensor Structures and Electronics Faculty of Electrical Engineering, University of Ljubljana Tržaška cesta 25, 1000, Ljubljana, Slovenia
| | - Pavel Janoš
- National Research Council of Italy (CNR)-, Institute of Materials (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR)-, Institute of Materials (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy
| |
Collapse
|
9
|
Sciortino G, Maréchal JD, Garribba E. Integrated experimental/computational approaches to characterize the systems formed by vanadium with proteins and enzymes. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01507e] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An integrated instrumental/computational approach to characterize metallodrug–protein adducts at the molecular level is reviewed. A series of applications are described, focusing on potential vanadium drugs with a generalization to other metals.
Collapse
Affiliation(s)
- Giuseppe Sciortino
- Departament de Química
- Universitat Autònoma de Barcelona
- Cerdanyola del Vallès
- Barcelona 08193
- Spain
| | - Jean-Didier Maréchal
- Departament de Química
- Universitat Autònoma de Barcelona
- Cerdanyola del Vallès
- Barcelona 08193
- Spain
| | - Eugenio Garribba
- Dipartimento di Chimica e Farmacia
- Università di Sassari
- 07100 Sassari
- Italy
| |
Collapse
|
10
|
Chen G, Seukep AJ, Guo M. Recent Advances in Molecular Docking for the Research and Discovery of Potential Marine Drugs. Mar Drugs 2020; 18:md18110545. [PMID: 33143025 PMCID: PMC7692358 DOI: 10.3390/md18110545] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/28/2022] Open
Abstract
Marine drugs have long been used and exhibit unique advantages in clinical practices. Among the marine drugs that have been approved by the Food and Drug Administration (FDA), the protein–ligand interactions, such as cytarabine–DNA polymerase, vidarabine–adenylyl cyclase, and eribulin–tubulin complexes, are the important mechanisms of action for their efficacy. However, the complex and multi-targeted components in marine medicinal resources, their bio-active chemical basis, and mechanisms of action have posed huge challenges in the discovery and development of marine drugs so far, which need to be systematically investigated in-depth. Molecular docking could effectively predict the binding mode and binding energy of the protein–ligand complexes and has become a major method of computer-aided drug design (CADD), hence this powerful tool has been widely used in many aspects of the research on marine drugs. This review introduces the basic principles and software of the molecular docking and further summarizes the applications of this method in marine drug discovery and design, including the early virtual screening in the drug discovery stage, drug target discovery, potential mechanisms of action, and the prediction of drug metabolism. In addition, this review would also discuss and prospect the problems of molecular docking, in order to provide more theoretical basis for clinical practices and new marine drug research and development.
Collapse
Affiliation(s)
- Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement & Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (G.C.); (A.J.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai 201203, China
| | - Armel Jackson Seukep
- Key Laboratory of Plant Germplasm Enhancement & Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (G.C.); (A.J.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai 201203, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, P.O. Box 63 Buea, Cameroon
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement & Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (G.C.); (A.J.S.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai 201203, China
- Correspondence: ; Tel.: +86-27-8770-0850
| |
Collapse
|
11
|
Pecina A, Eyrilmez SM, Köprülüoğlu C, Miriyala VM, Lepšík M, Fanfrlík J, Řezáč J, Hobza P. SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design. Chempluschem 2020; 85:2362-2371. [PMID: 32609421 DOI: 10.1002/cplu.202000120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/27/2020] [Indexed: 12/17/2022]
Abstract
Quantum mechanical (QM) methods have been gaining importance in structure-based drug design where a reliable description of protein-ligand interactions is of utmost significance. However, strategies i. e. QM/MM, fragmentation or semiempirical (SQM) methods had to be pursued to overcome the unfavorable scaling of QM methods. Various SQM-based approaches have significantly contributed to the accuracy of docking and improvement of lead compounds. Parametrizations of SQM and implicit solvent methods in our laboratory have been instrumental to obtain a reliable SQM-based scoring function. The experience gained in its application for activity ranking of ligands binding to tens of protein targets resulted in setting up a faster SQM/COSMO scoring approach, which outperforms standard scoring methods in native pose identification for two dozen protein targets with ten thousand poses. Recently, SQM/COSMO was effectively applied in a proof-of-concept study of enrichment in virtual screening. Due to its superior performance, feasibility and chemical generality, we propose the SQM/COSMO approach as an efficient tool in structure-based drug design.
Collapse
Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| |
Collapse
|
12
|
Abstract
There is significant potential for electronic structure methods to improve the quality of the predictions furnished by the tools of computer-aided drug design, which typically rely on empirically derived functions. In this perspective, we consider some recent examples of how quantum mechanics has been applied in predicting protein-ligand geometries, protein-ligand binding affinities and ligand strain on binding. We then outline several significant developments in quantum mechanics methodology likely to influence these approaches: in particular, we note the advent of more computationally expedient ab initio quantum mechanical methods that can provide chemical accuracy for larger molecular systems than hitherto possible. We highlight the emergence of increasingly accurate semiempirical quantum mechanical methods and the associated role of machine learning and molecular databases in their development. Indeed, the convergence of improved algorithms for solving and analyzing electronic structure, modern machine learning methods, and increasingly comprehensive benchmark data sets of molecular geometries and energies provides a context in which the potential of quantum mechanics will be increasingly realized in driving future developments and applications in structure-based drug discovery.
Collapse
Affiliation(s)
- Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Manchester, UK.
| |
Collapse
|
13
|
Horváth I, Jeszenői N, Bálint M, Paragi G, Hetényi C. A Fragmenting Protocol with Explicit Hydration for Calculation of Binding Enthalpies of Target-Ligand Complexes at a Quantum Mechanical Level. Int J Mol Sci 2019; 20:ijms20184384. [PMID: 31489952 PMCID: PMC6770515 DOI: 10.3390/ijms20184384] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 12/22/2022] Open
Abstract
Optimization of the enthalpy component of binding thermodynamics of drug candidates is a successful pathway of rational molecular design. However, the large size and missing hydration structure of target-ligand complexes often hinder such optimizations with quantum mechanical (QM) methods. At the same time, QM calculations are often necessitated for proper handling of electronic effects. To overcome the above problems, and help the QM design of new drugs, a protocol is introduced for atomic level determination of hydration structure and extraction of structures of target-ligand complex interfaces. The protocol is a combination of a previously published program MobyWat, an engine for assigning explicit water positions, and Fragmenter, a new tool for optimal fragmentation of protein targets. The protocol fostered a series of fast calculations of ligand binding enthalpies at the semi-empirical QM level. Ligands of diverse chemistry ranging from small aromatic compounds up to a large peptide helix of a molecular weight of 3000 targeting a leukemia protein were selected for systematic investigations. Comparison of various combinations of implicit and explicit water models demonstrated that the presence of accurately predicted explicit water molecules in the complex interface considerably improved the agreement with experimental results. A single scaling factor was derived for conversion of QM reaction heats into binding enthalpy values. The factor links molecular structure with binding thermodynamics via QM calculations. The new protocol and scaling factor will help automated optimization of binding enthalpy in future molecular design projects.
Collapse
Affiliation(s)
- István Horváth
- Chemistry Doctoral School, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary.
| | - Norbert Jeszenői
- Institute of Physiology, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Mónika Bálint
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Gábor Paragi
- MTA-SZTE Biomimetic Systems Research Group, Dóm tér 8, 6720 Szeged, Hungary.
- Institute of Physics, University of Pécs, Ifjúság útja 6, 7624 Pécs, Hungary.
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| |
Collapse
|
14
|
Advancing Drug Discovery via Artificial Intelligence. Trends Pharmacol Sci 2019; 40:592-604. [DOI: 10.1016/j.tips.2019.06.004] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/23/2019] [Accepted: 06/11/2019] [Indexed: 01/15/2023]
|
15
|
Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chem Rev 2019; 119:9478-9508. [DOI: 10.1021/acs.chemrev.9b00055] [Citation(s) in RCA: 578] [Impact Index Per Article: 115.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU−ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200122, China
- Department of Chemistry, New York University, New York, New York 10003, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
16
|
Najjar A, Platzer C, Luft A, Aßmann CA, Elghazawy NH, Erdmann F, Sippl W, Schmidt M. Computer-aided design, synthesis and biological characterization of novel inhibitors for PKMYT1. Eur J Med Chem 2018; 161:479-492. [PMID: 30388464 DOI: 10.1016/j.ejmech.2018.10.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/16/2018] [Accepted: 10/19/2018] [Indexed: 12/12/2022]
Abstract
In the current work, we applied computational methods to analyze the membrane-associated inhibitory kinase PKMYT1 and small molecule inhibitors. PKMYT1 regulates the cell cycle at G2/M transition and phosphorylates Thr14 and Tyr15 in the Cdk1-cyclin B complex. A combination of in silico and in vitro screening was applied to identify novel PKMYT1 inhibitors. The computational approach combined structural analysis, molecular docking, binding free energy calculations, and quantitative structure-activity relationship (QSAR) models. In addition, a computational fragment growing approach was applied to a set of previously identified diaminopyrimidines. Based on the derived computational models, several derivatives were synthesized and tested in vitro on PKMYT1. Novel inhibitors active in the sub-micromolar range were identified which provide the basis for further characterization of PKMYT1 as putative target for cancer therapy.
Collapse
Affiliation(s)
- Abdulkarim Najjar
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Charlott Platzer
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Anton Luft
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Chris Alexander Aßmann
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Nehal H Elghazawy
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Frank Erdmann
- Institute of Pharmacy, Department of Pharmacology, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Matthias Schmidt
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany.
| |
Collapse
|
17
|
|
18
|
Okimoto N, Otsuka T, Hirano Y, Taiji M. Use of the Multilayer Fragment Molecular Orbital Method to Predict the Rank Order of Protein-Ligand Binding Affinities: A Case Study Using Tankyrase 2 Inhibitors. ACS OMEGA 2018; 3:4475-4485. [PMID: 31458673 PMCID: PMC6641631 DOI: 10.1021/acsomega.8b00175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 03/23/2018] [Indexed: 06/10/2023]
Abstract
In computational drug discovery, ranking a series of compound analogues in the order that is consistent with the experimental binding affinities remains a challenge. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics (MM)-based force fields, although they cannot completely describe protein-ligand interactions. By contrast, quantum mechanics (QM) calculations play an important role in understanding the protein-ligand interactions; however, their huge computational costs hinder their application in drug discovery. In this study, we have evaluated the ability to rank the binding affinities of tankyrase 2 ligands by combining both MM and QM calculations. Our computational approach uses the protein-ligand binding energies obtained from a cost-effective multilayer fragment molecular orbital (MFMO) method combined with the solvation energy obtained from the MM-Poisson-Boltzmann/surface area (MM-PB/SA) method to predict the binding affinity. This approach enabled us to rank tankyrase 2 inhibitor analogues, outperforming several MM-based methods, including rescoring by molecular docking and the MM-PB/SA method alone. Our results show that this computational approach using the MFMO method is a promising tool for predicting the rank order of the binding affinities of inhibitor analogues.
Collapse
|
19
|
Wang Y, Liu J, Li J, He X. Fragment-based quantum mechanical calculation of protein-protein binding affinities. J Comput Chem 2018; 39:1617-1628. [PMID: 29707784 DOI: 10.1002/jcc.25236] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/02/2018] [Accepted: 04/01/2018] [Indexed: 12/13/2022]
Abstract
The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method has been successfully utilized for efficient linear-scaling quantum mechanical (QM) calculation of protein energies. In this work, we applied the EE-GMFCC method for calculation of binding affinity of Endonuclease colicin-immunity protein complex. The binding free energy changes between the wild-type and mutants of the complex calculated by EE-GMFCC are in good agreement with experimental results. The correlation coefficient (R) between the predicted binding energy changes and experimental values is 0.906 at the B3LYP/6-31G*-D level, based on the snapshot whose binding affinity is closest to the average result from the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) calculation. The inclusion of the QM effects is important for accurate prediction of protein-protein binding affinities. Moreover, the self-consistent calculation of PB solvation energy is required for accurate calculations of protein-protein binding free energies. This study demonstrates that the EE-GMFCC method is capable of providing reliable prediction of relative binding affinities for protein-protein complexes. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Yaqian Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Jinfeng Liu
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.,Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Jinjin Li
- Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano-electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.,National Engineering Research Centre for Nanotechnology, Shanghai, 200241, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| |
Collapse
|
20
|
Pecina A, Haldar S, Fanfrlík J, Meier R, Řezáč J, Lepšík M, Hobza P. SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein–Ligand Poses. J Chem Inf Model 2017; 57:127-132. [DOI: 10.1021/acs.jcim.6b00513] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Adam Pecina
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Susanta Haldar
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - René Meier
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Jan Řezáč
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Martin Lepšík
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Palacký University, 77146 Olomouc, Czech Republic
| |
Collapse
|
21
|
Wang M, Xie W, Li A, Xu S. Structural Basis and Mechanism of Chiral Benzedrine Molecules Interacting With Third Dopamine Receptor. Chirality 2016; 28:674-85. [PMID: 27581600 DOI: 10.1002/chir.22630] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 11/09/2022]
Abstract
In order to investigate the chiral benzedrine molecules corresponding to their different characteristics in biochemical systems, we studied their interaction with D3 R using the docking method, molecular dynamic simulation, and quantum chemistry. The obtained results indicate that the active residues for R-benzedrine (RAT) bound with D3 R are Ala132, Asp133, and Tyr55, while Asn57, Asp133, Asp168, Cys172, Gly54, Trp24, and Vall136 act as the active residues for S-benzedrine (SAT). The different active pockets are observed for ART or SAT because they possess different active residues. The binding energies between RAT and SAT with D3 R were determined to be -44.0 kJ.mol(-1) and -71.2 kJ.mol(-1) , respectively. These results demonstrate that SAT within the studied pocket of D3 R has a stronger capability of binding with D3 R, while it is more feasible for RAT to leave from the interior positions of D3 R. In addition, the results suggest that the D3 R protein can recognize chiral benzedrine molecules and influence their different addictive and pharmacological effects in biochemical systems. Chirality 28:674-685, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Ming Wang
- Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Wei Xie
- Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Aijing Li
- Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Sichuan Xu
- Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology, Yunnan University, Kunming, China.
| |
Collapse
|
22
|
Christensen A, Kubař T, Cui Q, Elstner M. Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chem Rev 2016; 116:5301-37. [PMID: 27074247 PMCID: PMC4867870 DOI: 10.1021/acs.chemrev.5b00584] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Indexed: 12/28/2022]
Abstract
Semiempirical (SE) methods can be derived from either Hartree-Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems.
Collapse
Affiliation(s)
- Anders
S. Christensen
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Tomáš Kubař
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Marcus Elstner
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| |
Collapse
|
23
|
Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chem Rev 2016; 116:5520-66. [DOI: 10.1021/acs.chemrev.5b00630] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
24
|
Pecina A, Meier R, Fanfrlík J, Lepšík M, Řezáč J, Hobza P, Baldauf C. The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein–ligand interactions and implicit COSMO solvation. Chem Commun (Camb) 2016; 52:3312-5. [DOI: 10.1039/c5cc09499b] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Strictly uphill – in cognate docking experiments we show that a quantum mechanical description of interaction and solvation outperforms established scoring functions in sharply distinguishing the native state from decoy poses.
Collapse
Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Sciences and IOCB Research Center
- 16610 Prague 6
- Czech Republic
| | - René Meier
- Institut für Biochemie
- Fakultät für Biowissenschaften
- Pharmazie und Psychologie
- Universität Leipzig
- D-04109 Leipzig
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Sciences and IOCB Research Center
- 16610 Prague 6
- Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Sciences and IOCB Research Center
- 16610 Prague 6
- Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Sciences and IOCB Research Center
- 16610 Prague 6
- Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Sciences and IOCB Research Center
- 16610 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft
- D-14195 Berlin
- Germany
| |
Collapse
|
25
|
TcCYPR04, a Cacao Papain-Like Cysteine-Protease Detected in Senescent and Necrotic Tissues Interacts with a Cystatin TcCYS4. PLoS One 2015; 10:e0144440. [PMID: 26641247 PMCID: PMC4671599 DOI: 10.1371/journal.pone.0144440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/18/2015] [Indexed: 11/19/2022] Open
Abstract
The interaction amongst papain-like cysteine-proteases (PLCP) and their substrates and inhibitors, such as cystatins, can be perceived as part of the molecular battlefield in plant-pathogen interaction. In cacao, four cystatins were identified and characterized by our group. We identified 448 proteases in cacao genome, whereof 134 were cysteine-proteases. We expressed in Escherichia coli a PLCP from cacao, named TcCYSPR04. Immunoblottings with anti-TcCYSPR04 exhibited protein increases during leaf development. Additional isoforms of TcCYSPR04 appeared in senescent leaves and cacao tissues infected by Moniliophthora perniciosa during the transition from the biotrophic to the saprophytic phase. TcCYSPR04 was induced in the apoplastic fluid of Catongo and TSH1188 cacao genotypes, susceptible and resistant to M. perniciosa, respectively, but greater intensity and additional isoforms were observed in TSH1188. The fungal protein MpNEP induced PLCP isoform expression in tobacco leaves, according to the cross reaction with anti-TcCYSPR04. Several protein isoforms were detected at 72 hours after treatment with MpNEP. We captured an active PLCP from cacao tissues, using a recombinant cacao cystatin immobilized in CNBr-Sepharose. Mass spectrometry showed that this protein corresponds to TcCYSPR04. A homology modeling was obtained for both proteins. In order to become active, TcCYSPR04 needs to lose its inhibitory domain. Molecular docking showed the physical-chemical complementarities of the interaction between the cacao enzyme and its inhibitor. We propose that TcCYSPR04 and its interactions with cacao cystatins are involved in the senescence and necrosis events related to witches' broom symptoms. This molecular interaction may be the target for future interventions to control witches' broom disease.
Collapse
|
26
|
Spyrakis F, Cavasotto CN. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Arch Biochem Biophys 2015; 583:105-19. [DOI: 10.1016/j.abb.2015.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 01/05/2023]
|
27
|
Otsuka T, Okimoto N, Taiji M. Assessment and acceleration of binding energy calculations for protein-ligand complexes by the fragment molecular orbital method. J Comput Chem 2015; 36:2209-18. [DOI: 10.1002/jcc.24055] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/17/2015] [Accepted: 07/30/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Takao Otsuka
- Laboratory for Computational Molecular Design, Computational Biology Research Core, RIKEN Quantitative Biology Center (QBiC); 1-6-5 Minatojima Minamimachi, Chuo-Ku, Kobe Hyogo 650-0047 Japan
| | - Noriaki Okimoto
- Laboratory for Computational Molecular Design, Computational Biology Research Core, RIKEN Quantitative Biology Center (QBiC); 1-6-5 Minatojima Minamimachi, Chuo-Ku, Kobe Hyogo 650-0047 Japan
| | - Makoto Taiji
- Laboratory for Computational Molecular Design, Computational Biology Research Core, RIKEN Quantitative Biology Center (QBiC); 1-6-5 Minatojima Minamimachi, Chuo-Ku, Kobe Hyogo 650-0047 Japan
| |
Collapse
|
28
|
Sampson C, Fox T, Tautermann CS, Woods C, Skylaris CK. A "Stepping Stone" Approach for Obtaining Quantum Free Energies of Hydration. J Phys Chem B 2015; 119:7030-40. [PMID: 25985723 DOI: 10.1021/acs.jpcb.5b01625] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We present a method which uses DFT (quantum, QM) calculations to improve free energies of binding computed with classical force fields (classical, MM). To overcome the incomplete overlap of configurational spaces between MM and QM, we use a hybrid Monte Carlo approach to generate quickly correct ensembles of structures of intermediate states between a MM and a QM/MM description, hence taking into account a great fraction of the electronic polarization of the quantum system, while being able to use thermodynamic integration to compute the free energy of transition between the MM and QM/MM. Then, we perform a final transition from QM/MM to full QM using a one-step free energy perturbation approach. By using QM/MM as a stepping stone toward the full QM description, we find very small convergence errors (<1 kJ/mol) in the transition to full QM. We apply this method to compute hydration free energies, and we obtain consistent improvements over the MM values for all molecules we used in this study. This approach requires large-scale DFT calculations as the full QM systems involved the ligands and all waters in their simulation cells, so the linear-scaling DFT code ONETEP was used for these calculations.
Collapse
Affiliation(s)
- Chris Sampson
- †School of Chemistry, University of Southampton, University Road, Southampton, Hampshire, SO17 1BJ, United Kingdom
| | | | | | - Christopher Woods
- §School of Chemistry, University of Bristol, Cantocks Close, Bristol, Somerset, BS8 1TS, United Kingdom
| | - Chris-Kriton Skylaris
- †School of Chemistry, University of Southampton, University Road, Southampton, Hampshire, SO17 1BJ, United Kingdom
| |
Collapse
|
29
|
Kurauchi R, Watanabe C, Fukuzawa K, Tanaka S. Novel type of virtual ligand screening on the basis of quantum-chemical calculations for protein–ligand complexes and extended clustering techniques. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.02.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
30
|
Rao H, Huangfu C, Wang Y, Wang X, Tang T, Zeng X, Li Z, Chen Y. Physicochemical Profiles of the Marketed Agrochemicals and Clues for Agrochemical Lead Discovery and Screening Library Development. Mol Inform 2015; 34:331-8. [DOI: 10.1002/minf.201400143] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/21/2015] [Indexed: 12/31/2022]
|
31
|
Wang Q, Edupuganti R, Tavares CDJ, Dalby KN, Ren P. Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis. Front Mol Biosci 2015; 2:9. [PMID: 25988177 PMCID: PMC4429643 DOI: 10.3389/fmolb.2015.00009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/03/2015] [Indexed: 01/09/2023] Open
Abstract
A-484954 is a known eEF2K inhibitor with submicromolar IC50 potency. However, the binding mechanism and the crystal structure of the kinase remains unknown. Here, we employ a homology eEF2K model, docking and alchemical free energy simulations to probe the binding mechanism of eEF2K, and in turn, guide the optimization of potential lead compounds. The inhibitor was docked into the ATP-binding site of a homology model first. Three different binding poses, hypothesis 1, 2, and 3, were obtained and subsequently applied to molecular dynamics (MD) based alchemical free energy simulations. The calculated relative binding free energy of the analogs of A-484954 using the binding pose of hypothesis 1 show a good correlation with the experimental IC50 values, yielding an r2 coefficient of 0.96 after removing an outlier (compound 5). Calculations using another two poses show little correlation with experimental data, (r2 of less than 0.5 with or without removing any outliers). Based on hypothesis 1, the calculated relative free energy suggests that bigger cyclic groups, at R1 e.g., cyclobutyl and cyclopentyl promote more favorable binding than smaller groups, such as cyclopropyl and hydrogen. Moreover, this study also demonstrates the ability of the alchemical free energy approach in combination with docking and homology modeling to prioritize compound synthesis. This can be an effective means of facilitating structure-based drug design when crystal structures are not available.
Collapse
Affiliation(s)
- Qiantao Wang
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin Austin, TX, USA ; Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin Austin, TX, USA
| | - Ramakrishna Edupuganti
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin Austin, TX, USA
| | - Clint D J Tavares
- Graduate Program in Cell and Molecular Biology, The University of Texas at Austin Austin, TX, USA
| | - Kevin N Dalby
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin Austin, TX, USA ; Graduate Program in Cell and Molecular Biology, The University of Texas at Austin Austin, TX, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin Austin, TX, USA
| |
Collapse
|
32
|
Karaman B, Sippl W. Docking and binding free energy calculations of sirtuin inhibitors. Eur J Med Chem 2015; 93:584-98. [PMID: 25748123 DOI: 10.1016/j.ejmech.2015.02.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/25/2015] [Accepted: 02/22/2015] [Indexed: 01/24/2023]
Abstract
Sirtuins form a unique and highly conserved class of NAD(+)-dependent lysine deacylases. Among these the human subtypes Sirt1-3 has been implicated in the pathogenesis of numerous diseases such as cancer, metabolic syndromes, viral diseases and neurological disorders. Most of the sirtuin inhibitors that have been identified so far show limited potency and/or isoform selectivity. Here, we introduce a promising method to generate protein-inhibitor complexes of human Sirt1, Sirt2 and Sirt3 by means of ligand docking and molecular dynamics simulations. This method highly reduces the complexity of such applications and can be applied to other protein targets beside sirtuins. To the best of our knowledge, we present the first binding free energy method developed by using a validated data set of sirtuin inhibitors, where both a fair number of compounds (33 thieno[3,2-d]pyrimidine-6-carboxamide derivatives) was developed and tested in the same laboratory and also crystal structures in complex with the enzyme have been reported. A significant correlation between binding free energies derived from MM-GBSA calculations and in vitro data was found for all three sirtuin subtypes. The developed MM-GBSA protocol is computationally inexpensive and can be applied as a post-docking filter in virtual screening to find novel Sirt1-3 inhibitors as well as to prioritize compounds with similar chemical structures for further biological characterization.
Collapse
Affiliation(s)
- Berin Karaman
- Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle, Saale, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle, Saale, Germany.
| |
Collapse
|
33
|
Chi S, Xie W, Zhang J, Xu S. Theoretical insight into the structural mechanism for the binding of vinblastine with tubulin. J Biomol Struct Dyn 2015; 33:2234-54. [PMID: 25588192 DOI: 10.1080/07391102.2014.999256] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Vinblastine (VLB) is one of vinca alkaloids with high cytotoxicity toward cancer cells approved for clinical use. However, because of drug resistance, toxicity, and other side effects caused from the use of VLB, new vinca alkaloids with higher cytotoxicity toward cancer cells and other good qualities need to develop. One strategy is to further study and better understand the essence why VLB possesses the high cytotoxicity toward cancer cells. In present work, by using molecular simulation, molecular docking, density functional calculation, and the crystal structure of α,β-tubulin complex, we find two modes labeled in catharanthine moiety (CM) and vindoline moiety (VM) modes of VLB bound with the interface of α,β-tubulin to probe the essence why VLB has the high cytotoxicity toward cancer cells. In the CM mode, nine key residues B-Ser178, B-Asp179, B-Glu183, B-Tyr210, B-Asp226, C-Lys326, C-Asp327, C-Lys336, and C-Lys352 from the α,β-tubulin complex are determined as the active sites for the interaction of VLB with α,β-tubulin. Some of them such as B-Ser178, B-Glu183, B-Tyr210, B-Asp226, C-Lys326, C-Asp327, and C-Lys336 are newly identified as the active sites in present work. The affinity between VLB and the active pocket within the interface of α,β-tubulin is -60.8 kJ mol(-1) in the CM mode. In the VM mode, that is a new mode established in present paper, nine similar key residues B-Lys176, B-Ser178, B-Asp179, B-Glu183, B-Tyr210, B-Asp226, C-Lys326, C-Asp327, and C-Lys336 from the α,β-tubulin complex are found as the active sites for the interaction with VLB. The difference is from one key residue C-Lys352 in the CM mode changed to the key residue B-Lys176 in the VM mode. The affinity between VLB and the active pocket within the interface of α,β-tubulin is -96.3 kJ mol(-1) in the VM mode. Based on the results obtained in present work, and because VLB looks like two faces, composed of CM and VM both to have similar polar active groups, to interact with the active sites, we suggest double-faces sticking mechanism for the binding of VLB to the interface of α,β-tubulin. The double-faces sticking mechanism can be used to qualitatively explain high cytotoxicity toward cancer cells of vinca alkaloids including vinblastine, vincristine, vindestine, and vinorelbine approved for clinical use and vinflunine still in a phase III clinical trial. Furthermore, this mechanism will be applied to develop novel vinca alkaloids with much higher cytotoxicity toward cancer cells.
Collapse
Affiliation(s)
- Shaoming Chi
- a Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource , College of Chemical Science and Technology, Yunnan University , Kunming 650091 , China
| | | | | | | |
Collapse
|
34
|
Multiscale quantum chemical approaches to QSAR modeling and drug design. Drug Discov Today 2014; 19:1921-7. [DOI: 10.1016/j.drudis.2014.09.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/01/2014] [Accepted: 09/26/2014] [Indexed: 12/24/2022]
|
35
|
Chaskar P, Zoete V, Röhrig UF. Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function. J Chem Inf Model 2014; 54:3137-52. [DOI: 10.1021/ci5004152] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prasad Chaskar
- Swiss Institute of Bioinformatics, Molecular Modeling Group,
Quartier Sorge, Bâtiment
Génopode, CH-1015 Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Molecular Modeling Group,
Quartier Sorge, Bâtiment
Génopode, CH-1015 Lausanne, Switzerland
| | - Ute F. Röhrig
- Swiss Institute of Bioinformatics, Molecular Modeling Group,
Quartier Sorge, Bâtiment
Génopode, CH-1015 Lausanne, Switzerland
| |
Collapse
|
36
|
Zhou ZG, Yao QZ, Lei D, Zhang QQ, Zhang J. Investigations on the mechanisms of interactions between matrix metalloproteinase 9 and its flavonoid inhibitors using a combination of molecular docking, hybrid quantum mechanical/molecular mechanical calculations, and molecular dynamics simulations. CAN J CHEM 2014. [DOI: 10.1139/cjc-2014-0180] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many experimental studies have found that flavonoids can inhibit the activities of matrix metalloproteinases (MMPs), but the relevant mechanisms are still unclear. In this paper, the interaction mechanisms of MMP-9 with its five flavonoid inhibitors are investigated using a combination of molecular docking, hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, and molecular dynamics simulations. The molecular dynamics simulation results show a good linear correlation between the calculated binding free energies of QM/MM−Poisson–Boltzmann surface area (PBSA) and the experimental −log(EC50) regarding the studied five flavonoids on MMP-9 inhibition in explicit solvent. It is found that compared with the MM−PBSA method, the QM/MM−PBSA method can obviously improve the accuracy for the calculated binding free energies. The predicted binding modes of the five flavonoid−MMP-9 complexes reveal that the different hydrogen bond networks can form besides producing the Zn−O coordination bonds, which can reasonably explain previous experimental results. The agreement between our calculated results and the previous experimental facts indicates that the force field parameters used here are effective and reliable for investigating the systems of flavonoid−MMP-9 interactions, and thus, these simulations and analyses could be reproduced for the other related systems involving protein−ligand interactions. This paper may be helpful for designing the new MMP-9 inhibitors having higher biological activities by carrying out the structural modifications of flavonoid molecules.
Collapse
Affiliation(s)
- Zhi-Guang Zhou
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Qi-Zheng Yao
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Dong Lei
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Qing-Qing Zhang
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Ji Zhang
- Department of Physical Chemistry, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| |
Collapse
|
37
|
Interaction energy analysis on specific binding of influenza virus hemagglutinin to avian and human sialosaccharide receptors: Importance of mutation-induced structural change. J Mol Graph Model 2014; 53:48-58. [DOI: 10.1016/j.jmgm.2014.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/04/2014] [Accepted: 07/07/2014] [Indexed: 11/19/2022]
|
38
|
Lindblom PR, Wu G, Liu Z, Jim KC, Baldwin JJ, Gregg RE, Claremon DA, Singh SB. An electronic environment and contact direction sensitive scoring function for predicting affinities of protein–ligand complexes in Contour ®. J Mol Graph Model 2014; 53:118-127. [DOI: 10.1016/j.jmgm.2014.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/06/2014] [Accepted: 07/14/2014] [Indexed: 12/15/2022]
|
39
|
Vidossich P, Magistrato A. QM/MM molecular dynamics studies of metal binding proteins. Biomolecules 2014; 4:616-45. [PMID: 25006697 PMCID: PMC4192665 DOI: 10.3390/biom4030616] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 11/16/2022] Open
Abstract
Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM)) simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu) and main group (Mg) metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.
Collapse
Affiliation(s)
- Pietro Vidossich
- Department of Chemistry, Autonomous University of Barcelona, 08193 Cerdanyola del Vallés, Spain.
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o, International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34165 Trieste, Italy.
| |
Collapse
|
40
|
Xu M, Lill MA. Induced fit docking, and the use of QM/MM methods in docking. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 10:e411-8. [PMID: 24050138 DOI: 10.1016/j.ddtec.2013.02.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Docking methods are popular computational techniques in drug discovery to identify new active molecules that bind to a given biological target. Although widely used, the predictive reliability of docking methods is often limited by the inability to accurately and efficiently model protein flexibility and quantify binding strength. We highlight several emerging concepts that address those methodological issues including a discussion on the incorporation of QM/MM methodologies in the scoring process.
Collapse
|
41
|
A systematic profile of clinical inhibitors responsive to EGFR somatic amino acid mutations in lung cancer: implication for the molecular mechanism of drug resistance and sensitivity. Amino Acids 2014; 46:1635-48. [DOI: 10.1007/s00726-014-1716-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 02/25/2014] [Indexed: 02/06/2023]
|
42
|
Ballester PJ, Schreyer A, Blundell TL. Does a more precise chemical description of protein-ligand complexes lead to more accurate prediction of binding affinity? J Chem Inf Model 2014; 54:944-55. [PMID: 24528282 PMCID: PMC3966527 DOI: 10.1021/ci500091r] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
![]()
Predicting
the binding affinities of large sets of diverse molecules against
a range of macromolecular targets is an extremely challenging task.
The scoring functions that attempt such computational prediction are
essential for exploiting and analyzing the outputs of docking, which
is in turn an important tool in problems such as structure-based drug
design. Classical scoring functions assume a predetermined theory-inspired
functional form for the relationship between the variables that describe
an experimentally determined or modeled structure of a protein–ligand
complex and its binding affinity. The inherent problem of this approach
is in the difficulty of explicitly modeling the various contributions
of intermolecular interactions to binding affinity. New scoring functions
based on machine-learning regression models, which are able to exploit
effectively much larger amounts of experimental data and circumvent
the need for a predetermined functional form, have already been shown
to outperform a broad range of state-of-the-art scoring functions
in a widely used benchmark. Here, we investigate the impact of the
chemical description of the complex on the predictive power of the
resulting scoring function using a systematic battery of numerical
experiments. The latter resulted in the most accurate scoring function
to date on the benchmark. Strikingly, we also found that a more precise
chemical description of the protein–ligand complex does not
generally lead to a more accurate prediction of binding affinity.
We discuss four factors that may contribute to this result: modeling
assumptions, codependence of representation and regression, data restricted
to the bound state, and conformational heterogeneity in data.
Collapse
Affiliation(s)
- Pedro J Ballester
- European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton - CB10 1SD, United Kingdom
| | | | | |
Collapse
|
43
|
Wichapong K, Rohe A, Platzer C, Slynko I, Erdmann F, Schmidt M, Sippl W. Application of Docking and QM/MM-GBSA Rescoring to Screen for Novel Myt1 Kinase Inhibitors. J Chem Inf Model 2014; 54:881-93. [DOI: 10.1021/ci4007326] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Kanin Wichapong
- Department of Pharmaceutical Chemistry and ‡Department of Pharmacology, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alexander Rohe
- Department of Pharmaceutical Chemistry and ‡Department of Pharmacology, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Charlott Platzer
- Department of Pharmaceutical Chemistry and ‡Department of Pharmacology, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Inna Slynko
- Department of Pharmaceutical Chemistry and ‡Department of Pharmacology, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Frank Erdmann
- Department of Pharmaceutical Chemistry and ‡Department of Pharmacology, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Matthias Schmidt
- Department of Pharmaceutical Chemistry and ‡Department of Pharmacology, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Wolfgang Sippl
- Department of Pharmaceutical Chemistry and ‡Department of Pharmacology, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| |
Collapse
|
44
|
Slynko I, Scharfe M, Rumpf T, Eib J, Metzger E, Schüle R, Jung M, Sippl W. Virtual screening of PRK1 inhibitors: ensemble docking, rescoring using binding free energy calculation and QSAR model development. J Chem Inf Model 2014; 54:138-50. [PMID: 24377786 DOI: 10.1021/ci400628q] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Protein kinase C Related Kinase 1 (PRK1) has been shown to be involved in the regulation of androgen receptor signaling and has been identified as a novel potential drug target for prostate cancer therapy. Since there is no PRK1 crystal structure available to date, multiple PRK1 homology models were generated in order to address the protein flexibility. An in-house library of compounds tested on PRK1 was docked into the ATP binding site of the generated models. In most cases a correct pose of the inhibitors could be identified by ensemble docking, while there is still a challenge of finding a reasonable scoring function that is able to rank compounds according to their biological activity. We estimated the binding free energy for our data set of structurally diverse PRK1 inhibitors using the MM-PB(GB)SA and QM/MM-GBSA methods. The obtained results demonstrate that a correlation between calculated binding free energies and experimental IC50 values was found to be usually higher than using docking scores. Furthermore, the developed approach was tested on a set of diverse PRK1 inhibitors taken from literature, which resulted in a significant correlation. The developed method is computationally inexpensive and can be applied as a postdocking filter in virtual screening as well as for optimization of PRK1 inhibitors in order to prioritize compounds for further biological characterization.
Collapse
Affiliation(s)
- Inna Slynko
- Institute of Pharmacy, MLU Halle-Wittenberg , 06120 Halle (Saale), Germany
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Fanfrlík J, Brahmkshatriya PS, Řezáč J, Jílková A, Horn M, Mareš M, Hobza P, Lepšík M. Quantum mechanics-based scoring rationalizes the irreversible inactivation of parasitic Schistosoma mansoni cysteine peptidase by vinyl sulfone inhibitors. J Phys Chem B 2013; 117:14973-82. [PMID: 24195769 DOI: 10.1021/jp409604n] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The quantum mechanics (QM)-based scoring function that we previously developed for the description of noncovalent binding in protein-ligand complexes has been modified and extended to treat covalent binding of inhibitory ligands. The enhancements are (i) the description of the covalent bond breakage and formation using hybrid QM/semiempirical QM (QM/SQM) restrained optimizations and (ii) the addition of the new ΔG(cov)' term to the noncovalent score, describing the "free" energy difference between the covalent and noncovalent complexes. This enhanced QM-based scoring function is applied to a series of 20 vinyl sulfone-based inhibitory compounds inactivating the cysteine peptidase cathepsin B1 of the Schistosoma mansoni parasite (SmCB1). The available X-ray structure of the SmCB1 in complex with a potent vinyl sulfone inhibitor K11017 is used as a template to build the other covalently bound complexes and to model the derived noncovalent complexes. We present the correlation of the covalent score and its constituents with the experimental binding data. Four outliers are identified. They contain bulky R1' substituents structurally divergent from the template, which might induce larger protein rearrangements than could be accurately modeled. In summary, we propose a new computational approach and an optimal protocol for the rapid evaluation and prospective design of covalent inhibitors with a conserved binding mode.
Collapse
Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, v.v.i., and Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Martin SF, Clements JH. Correlating structure and energetics in protein-ligand interactions: paradigms and paradoxes. Annu Rev Biochem 2013; 82:267-93. [PMID: 23746256 DOI: 10.1146/annurev-biochem-060410-105819] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Predicting protein-binding affinities of small molecules, even closely related ones, is a formidable challenge in biomolecular recognition and medicinal chemistry. A thermodynamic approach to optimizing affinity in protein-ligand interactions requires knowledge and understanding of how altering the structure of a small molecule will be manifested in protein-binding enthalpy and entropy changes; however, there is a relative paucity of such detailed information. In this review, we examine two strategies commonly used to increase ligand potency. The first of these involves introducing a cyclic constraint to preorganize a small molecule in its biologically active conformation, and the second entails adding nonpolar groups to a molecule to increase the amount of hydrophobic surface that is buried upon binding. Both of these approaches are motivated by paradigms suggesting that protein-binding entropy changes should become more favorable, but paradoxes can emerge that defy conventional wisdom.
Collapse
Affiliation(s)
- Stephen F Martin
- Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.
| | | |
Collapse
|
47
|
The Semiempirical Quantum Mechanical Scoring Function for In Silico Drug Design. Chempluschem 2013; 78:921-931. [DOI: 10.1002/cplu.201300199] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Indexed: 12/19/2022]
|
48
|
Rao L, Zhang IY, Guo W, Feng L, Meggers E, Xu X. Nonfitting protein-ligand interaction scoring function based on first-principles theoretical chemistry methods: Development and application on kinase inhibitors. J Comput Chem 2013; 34:1636-46. [DOI: 10.1002/jcc.23303] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 03/25/2013] [Accepted: 04/03/2013] [Indexed: 01/22/2023]
Affiliation(s)
| | | | | | - Li Feng
- Department of Chemistry; Philipps-University Marburg; Hans-Meerwein-Strasse; Marburg; 35032; Germany
| | | | | |
Collapse
|
49
|
Kiewisch K, Jacob CR, Visscher L. Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory. J Chem Theory Comput 2013; 9:2425-40. [DOI: 10.1021/ct3008759] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karin Kiewisch
- Amsterdam Center for Multiscale
Modeling, VU University Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
| | - Christoph R. Jacob
- Center for Functional Nanostructures
and Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe,
Germany
| | - Lucas Visscher
- Amsterdam Center for Multiscale
Modeling, VU University Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
| |
Collapse
|
50
|
Mucs D, Bryce RA. The application of quantum mechanics in structure-based drug design. Expert Opin Drug Discov 2013; 8:263-76. [DOI: 10.1517/17460441.2013.752812] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|