51
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Guardiani C, Cecconi F, Chiodo L, Cottone G, Malgaretti P, Maragliano L, Barabash ML, Camisasca G, Ceccarelli M, Corry B, Roth R, Giacomello A, Roux B. Computational methods and theory for ion channel research. ADVANCES IN PHYSICS: X 2022; 7:2080587. [PMID: 35874965 PMCID: PMC9302924 DOI: 10.1080/23746149.2022.2080587] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023] Open
Abstract
Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.
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Affiliation(s)
- C. Guardiani
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - F. Cecconi
- CNR - Istituto dei Sistemi Complessi, Rome, Italy and Istituto Nazionale di Fisica Nucleare, INFN, Roma1 section. 00185, Roma, Italy
| | - L. Chiodo
- Department of Engineering, Campus Bio-Medico University, Rome, Italy
| | - G. Cottone
- Department of Physics and Chemistry-Emilio Segrè, University of Palermo, Palermo, Italy
| | - P. Malgaretti
- Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Erlangen, Germany
| | - L. Maragliano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy, and Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - M. L. Barabash
- Department of Materials Science and Nanoengineering, Rice University, Houston, TX 77005, USA
| | - G. Camisasca
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
- Dipartimento di Fisica, Università Roma Tre, Rome, Italy
| | - M. Ceccarelli
- Department of Physics and CNR-IOM, University of Cagliari, Monserrato 09042-IT, Italy
| | - B. Corry
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - R. Roth
- Institut Für Theoretische Physik, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - A. Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - B. Roux
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago IL, USA
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52
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Dayl S, Schmid R. Fully Flexible Ligand Docking for the P2X7 Receptor Using ROSIE. Methods Mol Biol 2022; 2510:65-75. [PMID: 35776320 DOI: 10.1007/978-1-0716-2384-8_4] [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] [Indexed: 06/15/2023]
Abstract
The availability of P2X7 receptor structures with allosteric antagonists bound enables us to predict specific interactions between receptor and antagonists at atomistic detail. In this chapter we outline how modern ligand docking techniques can be employed by the nonexpert to predict putative binding modes for known or hypothetical allosteric P2X7 antagonists.
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Affiliation(s)
- Sudad Dayl
- Department of Chemistry, College of Science, University of Baghdad, Baghdad, Iraq
| | - Ralf Schmid
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.
- Leicester Institute of Structural and Chemical Biology (LISCB), University of Leicester, Leicester, UK.
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53
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Di Palma F, Decherchi S, Pardo-Avila F, Succi S, Levitt M, von Heijne G, Cavalli A. Probing Interplays between Human XBP1u Translational Arrest Peptide and 80S Ribosome. J Chem Theory Comput 2021; 18:1905-1914. [PMID: 34881571 PMCID: PMC8908735 DOI: 10.1021/acs.jctc.1c00796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
The ribosome stalling
mechanism is a crucial biological process,
yet its atomistic underpinning is still elusive. In this framework,
the human XBP1u translational arrest peptide (AP) plays a central
role in regulating the unfolded protein response (UPR) in eukaryotic
cells. Here, we report multimicrosecond all-atom molecular dynamics
simulations designed to probe the interactions between the XBP1u AP
and the mammalian ribosome exit tunnel, both for the wild type AP
and for four mutant variants of different arrest potencies. Enhanced
sampling simulations allow investigating the AP release process of
the different variants, shedding light on this complex mechanism.
The present outcomes are in qualitative/quantitative agreement with
available experimental data. In conclusion, we provide an unprecedented
atomistic picture of this biological process and clear-cut insights
into the key AP–ribosome interactions.
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Affiliation(s)
- Francesco Di Palma
- Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Sergio Decherchi
- Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Fátima Pardo-Avila
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, United States
| | - Sauro Succi
- Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy.,Center for Life Nano & Neurosciences at La Sapienza, Fondazione Istituto Italiano di Tecnologia, via Regina Elena, 295, I-00161 Roma, Italy.,Physics Department, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Michael Levitt
- Department of Structural Biology, Stanford University, Palo Alto, California 94305, United States
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
| | - Andrea Cavalli
- Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
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54
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Bhati AP, Wan S, Alfè D, Clyde AR, Bode M, Tan L, Titov M, Merzky A, Turilli M, Jha S, Highfield RR, Rocchia W, Scafuri N, Succi S, Kranzlmüller D, Mathias G, Wifling D, Donon Y, Di Meglio A, Vallecorsa S, Ma H, Trifan A, Ramanathan A, Brettin T, Partin A, Xia F, Duan X, Stevens R, Coveney PV. Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers. Interface Focus 2021; 11:20210018. [PMID: 34956592 PMCID: PMC8504892 DOI: 10.1098/rsfs.2021.0018] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2021] [Indexed: 12/13/2022] Open
Abstract
The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case, developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. The scale of the potential resulting workflow is such that it is dependent on supercomputing to achieve extremely high throughput. We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral compounds through repurposing on a variety of supercomputers.
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Affiliation(s)
- Agastya P. Bhati
- Centre for Computational Science, University College London, Gordon Street, London WC1H 0AJ, UK
| | - Shunzhou Wan
- Centre for Computational Science, University College London, Gordon Street, London WC1H 0AJ, UK
| | - Dario Alfè
- Department of Earth Sciences, London Centre for Nanotechnology and Thomas Young Centre at University College London, University College London, Gower Street, London WC1E 6BT, UK
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte Sant'Angelo, Napoli 80126, Italy
| | - Austin R. Clyde
- Department of Computer Science, University of Chicago, Chicago, IL, USA
| | - Mathis Bode
- Institute for Combustion Technology, RWTH Aachen University, Aachen 52056, Germany
| | - Li Tan
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Mikhail Titov
- Department of Electrical and Computer Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Andre Merzky
- Department of Electrical and Computer Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Matteo Turilli
- Department of Electrical and Computer Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Shantenu Jha
- Brookhaven National Laboratory, Upton, NY 11973, USA
- Department of Electrical and Computer Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | | | - Walter Rocchia
- Concept Lab, Italian Institute of Technology, Via Melen, Genova, Italy
| | - Nicola Scafuri
- Concept Lab, Italian Institute of Technology, Via Melen, Genova, Italy
| | - Sauro Succi
- Center for Life Nanosciences at La Sapienza, Italian Institute of Technology, viale Regina Elena, Roma, Italy
| | - Dieter Kranzlmüller
- Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences and Humanities, Boltzmannstrasse 1, Garching bei München 85748, Germany
| | - Gerald Mathias
- Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences and Humanities, Boltzmannstrasse 1, Garching bei München 85748, Germany
| | - David Wifling
- Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences and Humanities, Boltzmannstrasse 1, Garching bei München 85748, Germany
| | | | | | | | - Heng Ma
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Anda Trifan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Arvind Ramanathan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Tom Brettin
- Computing, Environment and Life Sciences Directorate, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Alexander Partin
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Fangfang Xia
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Xiaotan Duan
- Department of Computer Science, University of Chicago, Chicago, IL, USA
| | - Rick Stevens
- Computing, Environment and Life Sciences Directorate, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Peter V. Coveney
- Centre for Computational Science, University College London, Gordon Street, London WC1H 0AJ, UK
- Institute for Informatics, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
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55
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Zhang Q, Zhao N, Meng X, Yu F, Yao X, Liu H. The prediction of protein-ligand unbinding for modern drug discovery. Expert Opin Drug Discov 2021; 17:191-205. [PMID: 34731059 DOI: 10.1080/17460441.2022.2002298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Drug-target thermodynamic and kinetic information have perennially important roles in drug design. The prediction of protein-ligand unbinding, which can provide important kinetic information, in experiments continues to face great challenges. Uncovering protein-ligand unbinding through molecular dynamics simulations has become efficient and inexpensive with the progress and enhancement of computing power and sampling methods. AREAS COVERED In this review, various sampling methods for protein-ligand unbinding and their basic principles are firstly briefly introduced. Then, their applications in predicting aspects of protein-ligand unbinding, including unbinding pathways, dissociation rate constants, residence time and binding affinity, are discussed. EXPERT OPINION Although various sampling methods have been successfully applied in numerous systems, they still have shortcomings and deficiencies. Most enhanced sampling methods require researchers to possess a wealth of prior knowledge of collective variables or reaction coordinates. In addition, most systems studied at present are relatively simple, and the study of complex systems in real drug research remains greatly challenging. Through the combination of machine learning and enhanced sampling methods, prediction accuracy can be further improved, and some problems encountered in complex systems also may be solved.
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Affiliation(s)
| | - Nannan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaoxiao Meng
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Fansen Yu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China.,Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
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56
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Bernardi M, Ghaani MR, Bayazeid O. Phenylethanoid glycosides as a possible COVID-19 protease inhibitor: a virtual screening approach. J Mol Model 2021; 27:341. [PMID: 34731296 PMCID: PMC8565174 DOI: 10.1007/s00894-021-04963-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022]
Abstract
From the beginning of pandemic, more than 240 million people have been infected with a death rate higher than 2%. Indeed, the current exit strategy involving the spreading of vaccines must be combined with progress in effective treatment development. This scenario is sadly supported by the vaccine's immune activation time and the inequalities in the global immunization schedule. Bringing the crises under control means providing the world population with accessible and impactful new therapeutics. We screened a natural product library that contains a unique collection of 2370 natural products into the binding site of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro). According to the docking score and to the interaction at the active site, three phenylethanoid glycosides (forsythiaside A, isoacteoside, and verbascoside) were selected. In order to provide better insight into the atomistic interaction and test the impact of the three selected compounds at the binding site, we resorted to a half microsecond-long molecular dynamics simulation. As a result, we are showing that forsythiaside A is the most stable molecule and it is likely to possess the highest inhibitory effect against SARS-CoV-2 Mpro. Phenylethanoid glycosides also have been reported to have both protease and kinase activity. This kinase inhibitory activity is very beneficial in fighting viruses inside the body as kinases are required for viral entry, metabolism, and/or reproduction. The dual activity (kinase/protease) of phenylethanoid glycosides makes them very promising anit-COVID-19 agents.
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Affiliation(s)
- Mario Bernardi
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
- Department of Pharmacognosy, Faculty of Pharmacy, Hacettepe University, Ankara, 06100, Turkey
| | - Mohammad Reza Ghaani
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Omer Bayazeid
- Department of Pharmacognosy, Faculty of Pharmacy, Hacettepe University, Ankara, 06100, Turkey.
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57
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Wang P, Gao X, Zhang K, Pei Q, Xu X, Yan F, Dong J, Jing C. Exploring the binding mechanism of positive allosteric modulators in human metabotropic glutamate receptor 2 using molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:24125-24139. [PMID: 34596645 DOI: 10.1039/d1cp02157e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Positive allosteric modulators (PAMs) of human metabotropic glutamate receptor 2 (hmGlu2) are well-known in the treatment of psychiatric disorders for their higher selectivity and lower tolerance risk. A variety of PAMs have been reported over the last decade and two compounds were in Phase II clinical trials for schizophrenia and anxiety. These trials were discontinued on account of the unsatisfactory therapeutic efficacy, but PAMs were explored as novel treatments for addiction and epilepsy. Thus, it is still important to explore novel hmGlu2 PAMs in the near future. Nowadays, the challenges in optimizing drug potency and improving scaffold diversity for PAMs are the noncomprehensive character analyses of multiple scaffolds; the exploration of the binding modes of PAMs in the allosteric binding site have been proposed to reduce this difficulty. However, there has been no comprehensive research about the binding profiles of PAMs in the hmGlu2 receptor. To address this issue, this work explores the binding characters of eight PAMs representing five chemical series by multiple computational methods. As a result, the shared binding modes of the eight studied PAMs interacting with 15 residues in the allosteric binding site were defined. In addition, the reduced hydrophobicity with low electronegativity of R1, increased hydrophobicity with low negative electron density of R2 and the electronegativity of the linker were identified as indicators that regulate the affinity of PAMs. This finding agrees well with the physicochemical properties of reported multiple series PAMs. This comprehensive work sheds additional light on the binding mechanism and physicochemical regularity underlining PAMs affinity and could be further utilized as a structural and energetic blueprint for discovering and assessing novel PAMs for hmGlu2.
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Affiliation(s)
- Panpan Wang
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Xiaonan Gao
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Ke Zhang
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Qinglan Pei
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Xiaobo Xu
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Fengmei Yan
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Jianghong Dong
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Chenxi Jing
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
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58
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Diederichs T, Ahmad K, Burns JR, Nguyen QH, Siwy ZS, Tornow M, Coveney PV, Tampé R, Howorka S. Principles of Small-Molecule Transport through Synthetic Nanopores. ACS NANO 2021; 15:16194-16206. [PMID: 34596387 DOI: 10.1021/acsnano.1c05139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Synthetic nanopores made from DNA replicate the key biological processes of transporting molecular cargo across lipid bilayers. Understanding transport across the confined lumen of the nanopores is of fundamental interest and of relevance to their rational design for biotechnological applications. Here we reveal the transport principles of organic molecules through DNA nanopores by synergistically combining experiments and computer simulations. Using a highly parallel nanostructured platform, we synchronously measure the kinetic flux across hundreds of individual pores to obtain rate constants. The single-channel transport kinetics are close to the theoretical maximum, while selectivity is determined by the interplay of cargo charge and size, the pores' sterics and electrostatics, and the composition of the surrounding lipid bilayer. The narrow distribution of transport rates implies a high structural homogeneity of DNA nanopores. The molecular passageway through the nanopore is elucidated via coarse-grained constant-velocity steered molecular dynamics simulations. The ensemble simulations pinpoint with high resolution and statistical validity the selectivity filter within the channel lumen and determine the energetic factors governing transport. Our findings on these synthetic pores' structure-function relationship will serve to guide their rational engineering to tailor transport selectivity for cell biological research, sensing, and drug delivery.
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Affiliation(s)
- Tim Diederichs
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/M., 60438, Germany
| | - Katya Ahmad
- Centre for Computational Science, University College London, London, WC1H0AJ, England, U.K
| | - Jonathan R Burns
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, England, U.K
| | - Quoc Hung Nguyen
- Molecular Electronics, Technical University of Munich, Munich, 80333, Germany
| | - Zuzanna S Siwy
- School of Physical Sciences, University of California, Irvine, California 92697, United States
| | - Marc Tornow
- Molecular Electronics, Technical University of Munich, Munich, 80333, Germany
- Fraunhofer Research Institution for Microsystems and Solid State Technologies (EMFT), Munich, 80686, Germany
- Center of NanoScience (CeNS), Ludwig-Maximilian-University, Munich, 80539, Germany
| | - Peter V Coveney
- Centre for Computational Science, University College London, London, WC1H0AJ, England, U.K
- Informatics Institute, University of Amsterdam, Amsterdam, 1090 GH, The Netherlands
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/M., 60438, Germany
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, England, U.K
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59
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Şterbuleac D. Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators. RSC Med Chem 2021; 12:1503-1518. [PMID: 34671734 PMCID: PMC8459385 DOI: 10.1039/d1md00140j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/21/2021] [Indexed: 01/10/2023] Open
Abstract
Molecular dynamics (MD) simulations allow researchers to investigate the behavior of desired biological targets at ever-decreasing costs with ever-increasing precision. Among the biological macromolecules, ion channels are remarkable transmembrane proteins, capable of performing special biological processes and revealing a complex regulatory matrix, including modulation by small molecules, either endogenous or exogenous. Recently, given the developments in ion channel structure determination and accessibility of bio-computational techniques, MD and related tools are becoming increasingly popular in the intense research area regarding ligand-channel interactions. This review synthesizes and presents the most important fields of MD involvement in investigating channel-molecule interactions, including, but not limited to, deciphering the binding modes of ligands to their ion channel targets and the mechanisms through which chemical compounds exert their effect on channel function. Special attention is devoted to the importance of more elaborate methods, such as free energy calculations, while principles regarding drug design and discovery are highlighted. Several technical aspects involving the creation and simulation of channel-molecule MD systems (ligand parameterization, proper membrane setup, system building, etc.) are also presented.
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Affiliation(s)
- Daniel Şterbuleac
- Department of Health and Human Development, "Ştefan cel Mare" University of Suceava Str. Universităţii 13, 720229, E Building Suceava Romania
- Department of Forestry and Environmental Protection, "Ştefan cel Mare" University of Suceava Str. Universităţii 13, 720229, E Building Suceava Romania
- Integrated Center for Research, Development and Innovation in Advanced Materials, Nanotechnologies and Distributed Systems for Fabrication and Control (MANSiD), "Ştefan cel Mare" University of Suceava Str. Universităţii 13 720229 Suceava Romania
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60
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Vassaux M, Wan S, Edeling W, Coveney PV. Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation. J Chem Theory Comput 2021; 17:5187-5197. [PMID: 34280310 PMCID: PMC8389531 DOI: 10.1021/acs.jctc.1c00526] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Indexed: 11/29/2022]
Abstract
Classical molecular dynamics is a computer simulation technique that is in widespread use across many areas of science, from physics and chemistry to materials, biology, and medicine. The method continues to attract criticism due its oft-reported lack of reproducibility which is in part due to a failure to submit it to reliable uncertainty quantification (UQ). Here we show that the uncertainty arises from a combination of (i) the input parameters and (ii) the intrinsic stochasticity of the method controlled by the random seeds. To illustrate the situation, we make a systematic UQ analysis of a widely used molecular dynamics code (NAMD), applied to estimate binding free energy of a ligand-bound to a protein. In particular, we replace the usually fixed input parameters with random variables, systematically distributed about their mean values, and study the resulting distribution of the simulation output. We also perform a sensitivity analysis, which reveals that, out of a total of 175 parameters, just six dominate the variance in the code output. Furthermore, we show that binding energy calculations dampen the input uncertainty, in the sense that the variation around the mean output free energy is less than the variation around the mean of the assumed input distributions, if the output is ensemble-averaged over the random seeds. Without such ensemble averaging, the predicted free energy is five times more uncertain. The distribution of the predicted properties is thus strongly dependent upon the random seed. Owing to this substantial uncertainty, robust statistical measures of uncertainty in molecular dynamics simulation require the use of ensembles in all contexts.
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Affiliation(s)
- Maxime Vassaux
- Centre
for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
| | - Shunzhou Wan
- Centre
for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
| | - Wouter Edeling
- Centrum
Wiskunde & Informatica, Scientific Computing Group, Amsterdam 1090 GB, The Netherlands
| | - Peter V. Coveney
- Centre
for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
- Informatics
Institute, University of Amsterdam, Amsterdam 1012 WX, The Netherlands
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61
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Wan S, Kumar D, Ilyin V, Al Homsi U, Sher G, Knuth A, Coveney PV. The effect of protein mutations on drug binding suggests ensuing personalised drug selection. Sci Rep 2021; 11:13452. [PMID: 34188094 PMCID: PMC8241852 DOI: 10.1038/s41598-021-92785-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 06/09/2021] [Indexed: 11/08/2022] Open
Abstract
The advent of personalised medicine promises a deeper understanding of mechanisms and therefore therapies. However, the connection between genomic sequences and clinical treatments is often unclear. We studied 50 breast cancer patients belonging to a population-cohort in the state of Qatar. From Sanger sequencing, we identified several new deleterious mutations in the estrogen receptor 1 gene (ESR1). The effect of these mutations on drug treatment in the protein target encoded by ESR1, namely the estrogen receptor, was achieved via rapid and accurate protein-ligand binding affinity interaction studies which were performed for the selected drugs and the natural ligand estrogen. Four nonsynonymous mutations in the ligand-binding domain were subjected to molecular dynamics simulation using absolute and relative binding free energy methods, leading to the ranking of the efficacy of six selected drugs for patients with the mutations. Our study shows that a personalised clinical decision system can be created by integrating an individual patient's genomic data at the molecular level within a computational pipeline which ranks the efficacy of binding of particular drugs to variant proteins.
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Affiliation(s)
- Shunzhou Wan
- Department of Chemistry, Centre for Computational Science, University College London, London, WC1H 0AJ, UK
| | - Deepak Kumar
- Computational Biology, Carnegie Mellon University in Qatar (CMU-Q), Doha, Qatar
| | - Valentin Ilyin
- Computational Biology, Carnegie Mellon University in Qatar (CMU-Q), Doha, Qatar
| | - Ussama Al Homsi
- Hematology and Oncology Department, National Center for Cancer Care & Research, Hamad Medical Corporation, Doha, Qatar
| | - Gulab Sher
- Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Alexander Knuth
- Hematology and Oncology Department, National Center for Cancer Care & Research, Hamad Medical Corporation, Doha, Qatar
| | - Peter V Coveney
- Department of Chemistry, Centre for Computational Science, University College London, London, WC1H 0AJ, UK.
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Wan S, Sinclair RC, Coveney PV. Uncertainty quantification in classical molecular dynamics. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200082. [PMID: 33775140 PMCID: PMC8059622 DOI: 10.1098/rsta.2020.0082] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/02/2020] [Indexed: 05/24/2023]
Abstract
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach has begun to advance from being a computer-based means of rationalizing experimental observations to producing apparently credible predictions for a number of real-world applications within industrial sectors such as advanced materials and drug discovery. However, key aspects concerning the reproducibility of the method have not kept pace with the speed of its uptake in the scientific community. Here, we present a discussion of uncertainty quantification for molecular dynamics simulation designed to endow the method with better error estimates that will enable it to be used to report actionable results. The approach adopted is a standard one in the field of uncertainty quantification, namely using ensemble methods, in which a sufficiently large number of replicas are run concurrently, from which reliable statistics can be extracted. Indeed, because molecular dynamics is intrinsically chaotic, the need to use ensemble methods is fundamental and holds regardless of the duration of the simulations performed. We discuss the approach and illustrate it in a range of applications from materials science to ligand-protein binding free energy estimation. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'.
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, University College London, Gordon Street, London WC1H 0AJ, UK
| | - Robert C. Sinclair
- Centre for Computational Science, University College London, Gordon Street, London WC1H 0AJ, UK
| | - Peter V. Coveney
- Centre for Computational Science, University College London, Gordon Street, London WC1H 0AJ, UK
- Institute for Informatics, Science Park 904, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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63
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Hernández-Alvarez L, Oliveira AB, Hernández-González JE, Chahine J, Pascutti PG, de Araujo AS, de Souza FP. Computational study on the allosteric mechanism of Leishmania major IF4E-1 by 4E-interacting protein-1: Unravelling the determinants of m 7GTP cap recognition. Comput Struct Biotechnol J 2021; 19:2027-2044. [PMID: 33995900 PMCID: PMC8085901 DOI: 10.1016/j.csbj.2021.03.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023] Open
Abstract
Atomistic details on perturbations induced by Lm4E-IP1 binding are described. The modulation of LmIF4E-1 affinity for the cap is confirmed by energetic analyses. Signaling paths between the allosteric and othosteric sites of LmIF4E-1 are predicted. Lm4E-IP1 binding increases the side-chain entropy of W83 and R172 of LmIF4E-1. A mechanism of dynamic allostery is proposed for the regulation mediated by Lm4E-IP1.
During their life cycle, Leishmania parasites display a fine-tuned regulation of the mRNA translation through the differential expression of isoforms of eukaryotic translation initiation factor 4E (LeishIF4Es). The interaction between allosteric modulators such as 4E-interacting proteins (4E-IPs) and LeishIF4E affects the affinity of this initiation factor for the mRNA cap. Here, several computational approaches were employed to elucidate the molecular bases of the previously-reported allosteric modulation in L. major exerted by 4E-IP1 (Lm4E-IP1) on eukaryotic translation initiation factor 4E 1 (LmIF4E-1). Molecular dynamics (MD) simulations and accurate binding free energy calculations (ΔGbind) were combined with network-based modeling of residue-residue correlations. We also describe the differences in internal motions of LmIF4E-1 apo form, cap-bound, and Lm4E-IP1-bound systems. Through community network calculations, the differences in the allosteric pathways of allosterically-inhibited and active forms of LmIF4E-1 were revealed. The ΔGbind values show significant differences between the active and inhibited systems, which are in agreement with the available experimental data. Our study thoroughly describes the dynamical perturbations of LmIF4E-1 cap-binding site triggered by Lm4E-IP1. These findings are not only essential for the understanding of a critical process of trypanosomatids’ gene expression but also for gaining insight into the allostery of eukaryotic IF4Es, which could be useful for structure-based design of drugs against this protein family.
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Affiliation(s)
- Lilian Hernández-Alvarez
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Antonio B Oliveira
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil.,Center for Theoretical Biological Physics, Rice University, Huston, TX, United States
| | - Jorge Enrique Hernández-González
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil.,Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jorge Chahine
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Pedro Geraldo Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Suman de Araujo
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Fátima Pereira de Souza
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
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64
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Bieniek M, Bhati AP, Wan S, Coveney PV. TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing. J Chem Theory Comput 2021; 17:1250-1265. [PMID: 33486956 PMCID: PMC7876800 DOI: 10.1021/acs.jctc.0c01179] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Indexed: 12/14/2022]
Abstract
The TIES (Thermodynamic Integration with Enhanced Sampling) protocol is a formally exact alchemical approach in computational chemistry to the calculation of relative binding free energies. The validity of TIES relies on the correctness of matching atoms across compared pairs of ligands, laying the foundation for the transformation along an alchemical pathway. We implement a flexible topology superimposition algorithm which uses an exhaustive joint-traversal for computing the largest common component(s). The algorithm is employed to enable matching and morphing of partial rings in the TIES protocol along with a validation study using 55 transformations and five different proteins from our previous work. We find that TIES 20 with the RESP charge system, using the new superimposition algorithm, reproduces the previous results with mean unsigned error of 0.75 kcal/mol with respect to the experimental data. Enabling the morphing of partial rings decreases the size of the alchemical region in the dual-topology transformations resulting in a significant improvement in the prediction precision. We find that increasing the ensemble size from 5 to 20 replicas per λ window only has a minimal impact on the accuracy. However, the non-normal nature of the relative free energy distributions underscores the importance of ensemble simulation. We further compare the results with the AM1-BCC charge system and show that it improves agreement with the experimental data by slightly over 10%. This improvement is partly due to AM1-BCC affecting only the charges of the atoms local to the mutation, which translates to even fewer morphed atoms, consequently reducing issues with sampling and therefore ensemble averaging. TIES 20, in conjunction with the enablement of ring morphing, reduces the size of the alchemical region and significantly improves the precision of the predicted free energies.
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Affiliation(s)
- Mateusz
K. Bieniek
- Centre for Computational Science, Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Agastya P. Bhati
- Centre for Computational Science, Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Shunzhou Wan
- Centre for Computational Science, Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Peter V. Coveney
- Centre for Computational Science, Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
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Wan S, Potterton A, Husseini FS, Wright DW, Heifetz A, Malawski M, Townsend-Nicholson A, Coveney PV. Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors. Interface Focus 2020; 10:20190128. [PMID: 33178414 PMCID: PMC7653344 DOI: 10.1098/rsfs.2019.0128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
We apply the hit-to-lead ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and lead-optimization TIES (thermodynamic integration with enhanced sampling) methods to compute the binding free energies of a series of ligands at the A1 and A2A adenosine receptors, members of a subclass of the GPCR (G protein-coupled receptor) superfamily. Our predicted binding free energies, calculated using ESMACS, show a good correlation with previously reported experimental values of the ligands studied. Relative binding free energies, calculated using TIES, accurately predict experimentally determined values within a mean absolute error of approximately 1 kcal mol-1. Our methodology may be applied widely within the GPCR superfamily and to other small molecule-receptor protein systems.
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Andrew Potterton
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Fouad S. Husseini
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - David W. Wright
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Alexander Heifetz
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, UK
| | - Maciej Malawski
- ACK Cyfronet, AGH University of Science and Technology, Nawojki 11, 30-950, Kraków, Poland
| | - Andrea Townsend-Nicholson
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Peter V. Coveney
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, 1098XH Amsterdam, The Netherlands
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Zasada SJ, Wright DW, Coveney PV. Large-scale binding affinity calculations on commodity compute clouds. Interface Focus 2020; 10:20190133. [PMID: 33178415 PMCID: PMC7653340 DOI: 10.1098/rsfs.2019.0133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 01/31/2023] Open
Abstract
In recent years, it has become possible to calculate binding affinities of compounds bound to proteins via rapid, accurate, precise and reproducible free energy calculations. This is imperative in drug discovery as well as personalized medicine. This approach is based on molecular dynamics (MD) simulations and draws on sequence and structural information of the protein and compound concerned. Free energies are determined by ensemble averages of many MD replicas, each of which requires hundreds of cores and/or GPU accelerators, which are now available on commodity cloud computing platforms; there are also requirements for initial model building and subsequent data analysis stages. To automate the process, we have developed a workflow known as the binding affinity calculator. In this paper, we focus on the software infrastructure and interfaces that we have developed to automate the overall workflow and execute it on commodity cloud platforms, in order to reliably predict their binding affinities on time scales relevant to the domains of application, and illustrate its application to two free energy methods.
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Affiliation(s)
| | | | - P. V. Coveney
- Centre for Computational Science, University College London, 20 Gordon Street, London WC1H 0AJ, UK
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67
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Affiliation(s)
- Peter V. Coveney
- Centre for Computational Science, University College London, London, UK
- Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
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