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Shaimardanov AR, Shulga DA, Palyulin VA. Do electrostatic interactions make a difference in physics-based AutoDock4 scoring function? J Comput Chem 2024; 45:1806-1820. [PMID: 38661234 DOI: 10.1002/jcc.27373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Physics-based scoring function AutoDock4 is one of the most successfully applied tools in the area of structure-based drug design. However, current scoring functions are still far from being perfect. In a recent work highlighting the strengths and deficiencies of current scoring functions, we discovered that the residual error of ΔGbind predictions made by AutoDock4 is highly correlated to the presence of formally charged fragments in a ligand. In this work, we study how the use of the high-quality atomic charges, applied for contemporary force fields calculation, affects the quality of the experimental ΔGbind prediction by means of AutoDock4. We initially expected that the previously found discrepancy could be attributed to the Gasteiger charges used within AutoDock4. We show that AutoDock4 is, surprisingly, not sensitive to the charges used, and the use of QC-derived atomic charges does not lead to any statistical improvements. We also briefly discuss the role of the explicit empirical hydrogen bond term along with the electrostatic term.
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Affiliation(s)
- Arslan R Shaimardanov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Dmitry A Shulga
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Vladimir A Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
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Broni E, Ashley C, Adams J, Manu H, Aikins E, Okom M, Miller WA, Wilson MD, Kwofie SK. Cheminformatics-Based Study Identifies Potential Ebola VP40 Inhibitors. Int J Mol Sci 2023; 24:ijms24076298. [PMID: 37047270 PMCID: PMC10094735 DOI: 10.3390/ijms24076298] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
The Ebola virus (EBOV) is still highly infectious and causes severe hemorrhagic fevers in primates. However, there are no regulatorily approved drugs against the Ebola virus disease (EVD). The highly virulent and lethal nature of EVD highlights the need to develop therapeutic agents. Viral protein 40 kDa (VP40), the most abundantly expressed protein during infection, coordinates the assembly, budding, and release of viral particles into the host cell. It also regulates viral transcription and RNA replication. This study sought to identify small molecules that could potentially inhibit the VP40 protein by targeting the N-terminal domain using an in silico approach. The statistical quality of AutoDock Vina’s capacity to discriminate between inhibitors and decoys was determined, and an area under the curve of the receiver operating characteristic (AUC-ROC) curve of 0.791 was obtained. A total of 29,519 natural-product-derived compounds from Chinese and African sources as well as 2738 approved drugs were successfully screened against VP40. Using a threshold of −8 kcal/mol, a total of 7, 11, 163, and 30 compounds from the AfroDb, Northern African Natural Products Database (NANPDB), traditional Chinese medicine (TCM), and approved drugs libraries, respectively, were obtained after molecular docking. A biological activity prediction of the lead compounds suggested their potential antiviral properties. In addition, random-forest- and support-vector-machine-based algorithms predicted the compounds to be anti-Ebola with IC50 values in the micromolar range (less than 25 μM). A total of 42 natural-product-derived compounds were identified as potential EBOV inhibitors with desirable ADMET profiles, comprising 1, 2, and 39 compounds from NANPDB (2-hydroxyseneganolide), AfroDb (ZINC000034518176 and ZINC000095485942), and TCM, respectively. A total of 23 approved drugs, including doramectin, glecaprevir, velpatasvir, ledipasvir, avermectin B1, nafarelin acetate, danoprevir, eltrombopag, lanatoside C, and glycyrrhizin, among others, were also predicted to have potential anti-EBOV activity and can be further explored so that they may be repurposed for EVD treatment. Molecular dynamics simulations coupled with molecular mechanics Poisson–Boltzmann surface area calculations corroborated the stability and good binding affinities of the complexes (−46.97 to −118.9 kJ/mol). The potential lead compounds may have the potential to be developed as anti-EBOV drugs after experimental testing.
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Affiliation(s)
- Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Carolyn Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Joseph Adams
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
| | - Hammond Manu
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Ebenezer Aikins
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Mary Okom
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology and Neuroscience, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence: (W.A.M.III); (S.K.K.); Tel.: +1(708)-2168451 (W.A.M.III); +23-320-3797922 (S.K.K.)
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana
- Correspondence: (W.A.M.III); (S.K.K.); Tel.: +1(708)-2168451 (W.A.M.III); +23-320-3797922 (S.K.K.)
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Shahfar H, O'Brien CJ, Budyak IL, Roberts CJ. Predicting Experimental B22 Values and the Effects of Histidine Charge States for Monoclonal Antibodies Using Coarse-Grained Molecular Simulations. Mol Pharm 2022; 19:3820-3830. [PMID: 36194430 DOI: 10.1021/acs.molpharmaceut.2c00337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Static light scattering (SLS) was used to characterize five monoclonal antibodies (MAbs) as a function of total ionic strength (TIS) at pH values between 5.5 and 7.0. Second osmotic virial coefficient (B22) values were determined experimentally for each MAb as a function of TIS using low protein concentration SLS data. Coarse-grained molecular simulations were performed to predict the B22 values for each MAb at a given pH and TIS. To include the effect of charge fluctuations of titratable residues in the B22 calculations, a statistical approach was introduced in the Monte Carlo algorithm based on the protonation probability based on a given pH value and the Henderson-Hasselbalch equation. The charged residues were allowed to fluctuate individually, based on the sampled microstates and the influence of electrostatic interactions on net protein-protein interactions during the simulations. Compared to static charge simulations, the new approach provided improved results compared to experimental B22 values at pH conditions near the pKa of titratable residues.
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Affiliation(s)
- Hassan Shahfar
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware19716, United States
| | - Christopher J O'Brien
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware19716, United States
| | - Ivan L Budyak
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana46285, United States
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware19716, United States
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Sun S, Huggins DJ. Assessing the effect of forcefield parameter sets on the accuracy of relative binding free energy calculations. Front Mol Biosci 2022; 9:972162. [PMID: 36225254 PMCID: PMC9549959 DOI: 10.3389/fmolb.2022.972162] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Software for accurate prediction of protein-ligand binding affinity can be a key enabling tool for small molecule drug discovery. Free energy perturbation (FEP) is a computational technique that can be used to compute binding affinity differences between molecules in a congeneric series. It has shown promise in reliably generating accurate predictions and is now widely used in the pharmaceutical industry. However, the high computational cost and use of commercial software, together with the technical challenges to setup, run, and analyze the simulations, limits the usage of FEP. Here, we use an automated FEP workflow which uses the open-source OpenMM package. To enable effective application of FEP, we compared the performance of different water models, partial charge assignments, and AMBER protein forcefields in eight benchmark test cases previously assembled for FEP validation studies.
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Affiliation(s)
- Shan Sun
- Tri-Institutional Therapeutics Discovery Institute, New York, NY, United States
| | - David J. Huggins
- Tri-Institutional Therapeutics Discovery Institute, New York, NY, United States
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, United States
- *Correspondence: David J. Huggins,
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Titov IY, Stroylov VS, Rusina P, Svitanko IV. Preliminary modelling as the first stage of targeted organic synthesis. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The review aims to present a classification and applicability analysis of methods for preliminary molecular modelling for targeted organic, catalytic and biocatalytic synthesis. The following three main approaches are considered as a primary classification of the methods: modelling of the target – ligand coordination without structural information on both the target and the resulting complex; calculations based on experimentally obtained structural information about the target; and dynamic simulation of the target – ligand complex and the reaction mechanism with calculation of the free energy of the reaction. The review is meant for synthetic chemists to be used as a guide for building an algorithm for preliminary modelling and synthesis of structures with specified properties.
The bibliography includes 353 references.
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Wade AD, Huggins DJ. Identification of Optimal Ligand Growth Vectors Using an Alchemical Free-Energy Method. J Chem Inf Model 2020; 60:5580-5594. [PMID: 32810401 DOI: 10.1021/acs.jcim.0c00610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, a novel method to rationally design inhibitors with improved steric contacts and enhanced binding free energies is presented. This new method uses alchemical single step perturbation calculations to rapidly optimize the van der Waals interactions of a small molecule in a protein-ligand complex in order to maximize its binding affinity. The results of the optimizer are used to predict beneficial growth vectors on the ligand, and good agreement is found between the predictions from the optimizer and a more rigorous free energy calculation, with a Spearman's rank order correlation of 0.59. The advantage of the method presented here is the significant speed up of over 10-fold compared to traditional free energy calculations and sublinear scaling with the number of growth vectors assessed. Where experimental data were available, mutations from hydrogen to a methyl group at sites highlighted by the optimizer were calculated with MBAR, and the mean unsigned error between experimental and calculated values of the binding free energy was 0.83 kcal/mol.
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Affiliation(s)
- Alexander D Wade
- TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - David J Huggins
- Tri-Institutional Therapeutics Discovery Institute, Belfer Research Building, 413 East 69th Street, 16th Floor, Box 300, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
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Dittner M, Hartke B. Globally optimal catalytic fields for a Diels-Alder reaction. J Chem Phys 2020; 152:114106. [PMID: 32199410 DOI: 10.1063/1.5142839] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In a previous paper [M. Dittner and B. Hartke, J. Chem. Theory Comput. 14, 3547 (2018)], we introduced a preliminary version of our GOCAT (globally optimal catalyst) concept in which electrostatic catalysts are designed for arbitrary reactions by global optimization of distributed point charges that surround the reaction. In this first version, a pre-defined reaction path was kept fixed. This unrealistic assumption allowed for only small catalytic effects. In the present work, we extend our GOCAT framework by a sophisticated and robust on-the-fly reaction path optimization, plus further concomitant algorithm adaptions. This allows smaller and larger excursions from a pre-defined reaction path under the influence of the GOCAT point-charge surrounding, all the way to drastic mechanistic changes. In contrast to the restricted first GOCAT version, this new version is able to address real-life catalysis. We demonstrate this by applying it to the electrostatic catalysis of a prototypical Diels-Alder reaction. Without using any prior information, this procedure re-discovers theoretically and experimentally established features of electrostatic catalysis of this very reaction, including a field-dependent transition from the synchronous, concerted textbook mechanism to a zwitterionic two-step mechanism, and diastereomeric discrimination by suitable electric field components.
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Affiliation(s)
- Mark Dittner
- Institute for Physical Chemistry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany
| | - Bernd Hartke
- Institute for Physical Chemistry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany
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