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Zia SR, Coricello A, Bottegoni G. Increased throughput in methods for simulating protein ligand binding and unbinding. Curr Opin Struct Biol 2024; 87:102871. [PMID: 38924980 DOI: 10.1016/j.sbi.2024.102871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
By incorporating full flexibility and enabling the quantification of crucial parameters such as binding free energies and residence times, methods for investigating protein-ligand binding and unbinding via molecular dynamics provide details on the involved mechanisms at the molecular level. While these advancements hold promise for impacting drug discovery, a notable drawback persists: their relatively time-consuming nature limits throughput. Herein, we survey recent implementations which, employing a blend of enhanced sampling techniques, a clever choice of collective variables, and often machine learning, strive to enhance the efficiency of new and previously reported methods without compromising accuracy. Particularly noteworthy is the validation of these methods that was often performed on systems mirroring real-world drug discovery scenarios.
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Affiliation(s)
- Syeda Rehana Zia
- Department of Paediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, 74800, Pakistan
| | - Adriana Coricello
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, 61029, Italy.
| | - Giovanni Bottegoni
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, 61029, Italy; Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, B15 2TT, United Kingdom.
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2
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Hao D, Niu LN. Computational Study on the Wealth Conformations of Hepatitis C Virus Envelope Glycoprotein 2 and Role of Its Glycan Coat. J Chem Inf Model 2024; 64:4811-4821. [PMID: 38861660 DOI: 10.1021/acs.jcim.4c00521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Hepatitis C virus (HCV) is a major cause of chronic liver disease and hepatocellular carcinoma. Antibody development efforts mainly revolve around HCV envelope glycoprotein 2 (E2), which mediates host cell entry by interacting with several cell surface receptors, including CD81. We still have limited knowledge about the structural ensembles and the dynamic behavior of both the CD81 binding sites and the glycans on E2. Here, multiple microsecond-long, all-atom molecular dynamics (MD) simulations, as well as a Markov state model (MSM), were performed to provide an atomistic perspective on the dynamic nature of E2 and its glycans. End-to-end accessibility analyses outline a complete overview of the vulnerabilities of the glycan shield of E2, which may be exploited in therapeutic efforts. Additionally, the Markov state model built from the simulation maps four metastable states for AS412 and three metastable states for the front layer in CD81 binding sites, while binding with HEPC3 would induce a conformation selection for both of them. Overall, this work presents hitherto unseen functional and structural insights into E2 and its glycan coat, providing a new theoretical foundation to control the conformational plasticity of E2 that could be harnessed for vaccine development.
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Affiliation(s)
- Dongxiao Hao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an 710032, China
- School of Electronics and Information Engineering, Ankang University, Ankang 725000, China
| | - Li-Na Niu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an 710032, China
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3
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Marques S, Kouba P, Legrand A, Sedlar J, Disson L, Planas-Iglesias J, Sanusi Z, Kunka A, Damborsky J, Pajdla T, Prokop Z, Mazurenko S, Sivic J, Bednar D. CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules. JACS AU 2024; 4:2228-2245. [PMID: 38938816 PMCID: PMC11200249 DOI: 10.1021/jacsau.4c00182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/24/2024] [Accepted: 05/13/2024] [Indexed: 06/29/2024]
Abstract
Computational study of the effect of drug candidates on intrinsically disordered biomolecules is challenging due to their vast and complex conformational space. Here, we developed a comparative Markov state analysis (CoVAMPnet) framework to quantify changes in the conformational distribution and dynamics of a disordered biomolecule in the presence and absence of small organic drug candidate molecules. First, molecular dynamics trajectories are generated using enhanced sampling, in the presence and absence of small molecule drug candidates, and ensembles of soft Markov state models (MSMs) are learned for each system using unsupervised machine learning. Second, these ensembles of learned MSMs are aligned across different systems based on a solution to an optimal transport problem. Third, the directional importance of inter-residue distances for the assignment to different conformational states is assessed by a discriminative analysis of aggregated neural network gradients. This final step provides interpretability and biophysical context to the learned MSMs. We applied this novel computational framework to assess the effects of ongoing phase 3 therapeutics tramiprosate (TMP) and its metabolite 3-sulfopropanoic acid (SPA) on the disordered Aβ42 peptide involved in Alzheimer's disease. Based on adaptive sampling molecular dynamics and CoVAMPnet analysis, we observed that both TMP and SPA preserved more structured conformations of Aβ42 by interacting nonspecifically with charged residues. SPA impacted Aβ42 more than TMP, protecting α-helices and suppressing the formation of aggregation-prone β-strands. Experimental biophysical analyses showed only mild effects of TMP/SPA on Aβ42 and activity enhancement by the endogenous metabolization of TMP into SPA. Our data suggest that TMP/SPA may also target biomolecules other than Aβ peptides. The CoVAMPnet method is broadly applicable to study the effects of drug candidates on the conformational behavior of intrinsically disordered biomolecules.
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Affiliation(s)
- Sérgio
M. Marques
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Petr Kouba
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- Czech
Institute of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, Dejvice, Praha 6 160 00, Czech Republic
- Faculty
of Electrical Engineering, Czech Technical
University in Prague, Technicka 2, Dejvice, Praha 6 166 27, Czech Republic
| | - Anthony Legrand
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Jiri Sedlar
- Czech
Institute of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, Dejvice, Praha 6 160 00, Czech Republic
| | - Lucas Disson
- Czech
Institute of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, Dejvice, Praha 6 160 00, Czech Republic
| | - Joan Planas-Iglesias
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Zainab Sanusi
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Antonin Kunka
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Tomas Pajdla
- Czech
Institute of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, Dejvice, Praha 6 160 00, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Stanislav Mazurenko
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Josef Sivic
- Czech
Institute of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, Dejvice, Praha 6 160 00, Czech Republic
| | - David Bednar
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
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Spiriti J, Wong CF. Quantitative Prediction of Dissociation Rates of PYK2 Ligands Using Umbrella Sampling and Milestoning. J Chem Theory Comput 2024; 20:4029-4044. [PMID: 38640609 DOI: 10.1021/acs.jctc.4c00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
We used umbrella sampling and the milestoning simulation method to study the dissociation of multiple ligands from protein kinase PYK2. The activation barriers obtained from the potential of mean force of the umbrella sampling simulations correlated well with the experimental dissociation rates. Using the zero-temperature string method, we obtained optimized paths along the free-energy surfaces for milestoning simulations of three ligands with a similar structure. The milestoning simulations gave an absolute dissociation rate within 2 orders of magnitude of the experimental value for two ligands but at least 3 orders of magnitude too high for the third. Despite the similarity in their structures, the ligands took different pathways to exit from the binding site of PYK2, making contact with different sets of residues. In addition, the protein experienced different conformational changes for dissociation of the three ligands.
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Affiliation(s)
- Justin Spiriti
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri 63121, United States
| | - Chung F Wong
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri 63121, United States
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Dutta S, Shukla D. Characterization of binding kinetics and intracellular signaling of new psychoactive substances targeting cannabinoid receptor using transition-based reweighting method. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.29.560261. [PMID: 37873328 PMCID: PMC10592854 DOI: 10.1101/2023.09.29.560261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
New psychoactive substances (NPS) targeting cannabinoid receptor 1 pose a significant threat to society as recreational abusive drugs that have pronounced physiological side effects. These greater adverse effects compared to classical cannabinoids have been linked to the higher downstream β-arrestin signaling. Thus, understanding the mechanism of differential signaling will reveal important structure-activity relationship essential for identifying and potentially regulating NPS molecules. In this study, we simulate the slow (un)binding process of NPS MDMB-Fubinaca and classical cannabinoid HU-210 from CB1 using multi-ensemble simulation to decipher the effects of ligand binding dynamics on downstream signaling. The transition-based reweighing method is used for the estimation of transition rates and underlying thermodynamics of (un)binding processes of ligands with nanomolar affinities. Our analyses reveal major interaction differences with transmembrane TM7 between NPS and classical cannabinoids. A variational autoencoder-based approach, neural relational inference (NRI), is applied to assess the allosteric effects on intracellular regions attributable to variations in binding pocket interactions. NRI analysis indicate a heightened level of allosteric control of NPxxY motif for NPS-bound receptors, which contributes to the higher probability of formation of a crucial triad interaction (Y7.53-Y5.58-T3.46) necessary for stronger β-arrestin signaling. Hence, in this work, MD simulation, data-driven statistical methods, and deep learning point out the structural basis for the heightened physiological side effects associated with NPS, contributing to efforts aimed at mitigating their public health impact.
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Affiliation(s)
- Soumajit Dutta
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
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6
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Xu T, Li Y, Gao X, Zhang L. Understanding the Fast-Triggering Unfolding Dynamics of FK-11 upon Photoexcitation of Azobenzene. J Phys Chem Lett 2024; 15:3531-3540. [PMID: 38526058 DOI: 10.1021/acs.jpclett.4c00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Photoswitchable molecules can control the activity and functions of biomolecules by triggering conformational changes. However, it is still challenging to fully understand such fast-triggering conformational evolution from nonequilibrium to equilibrium distribution at the molecular level. Herein, we successfully simulated the unfolding of the FK-11 peptide upon the photoinduced trans-to-cis isomerization of azobenzene based on the Markov state model. We found that the ensemble of FK-11 contains five conformational states, constituting two unfolding pathways. More intriguingly, we observed the microsecond-scale conformational propagation of the FK-11 peptide from the fully folded state to the equilibrium populations of the five states. The computed CD spectra match well with the experimental data, validating our simulation method. Overall, our study not only offers a protocol to study the photoisomerization-induced conformational changes of enzymes but also could orientate the rational design of a photoswitchable molecule to manipulate biological functions.
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Affiliation(s)
- Tiantian Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongfang Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Xin Gao
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Fuzhou, Fujian 361005, China
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Wong CF. 15 Years of molecular simulation of drug-binding kinetics. Expert Opin Drug Discov 2023; 18:1333-1348. [PMID: 37789731 PMCID: PMC10926948 DOI: 10.1080/17460441.2023.2264770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/26/2023] [Indexed: 10/05/2023]
Abstract
INTRODUCTION Drug-binding kinetics has been increasingly recognized as an important factor to be considered in drug discovery. Long residence time could prolong the action of some drugs while produce toxicity on others. Early evaluation of the binding kinetics of drug candidates could reduce attrition rate late in the drug discovery process. Computational prediction of drug-binding kinetics is useful as compounds can be evaluated even before they are made. However, simulation of drug-binding kinetics is a challenging problem because of the long-time scale involved. Nevertheless, significant progress has been made. AREAS COVERED This review illustrates the rapid evolution of qualitative to quantitative molecular dynamics-based methods that have been developed over the last 15 years. EXPERT OPINION The development of new methods based on molecular dynamics simulations now enables computation of absolute association/dissociation rate constants. Cheaper methods capable of identifying candidates with fast or slow binding kinetics, or rank-ordering rate constants are also available. Together, these methods have generated useful insights into the molecular mechanisms of drug-binding kinetics, and the design of drug candidates with therapeutically favorable kinetics. Although predicting absolute rate constants is still expensive and challenging, rapid improvement is expected in the coming years with the continuing refinement of current technologies, development of new methodologies, and the utilization of machine learning.
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Affiliation(s)
- Chung F Wong
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, MO, USA
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Ojha AA, Srivastava A, Votapka LW, Amaro RE. Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations. J Chem Inf Model 2023; 63:2469-2482. [PMID: 37023323 PMCID: PMC10131228 DOI: 10.1021/acs.jcim.2c01589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Janus kinases (JAK), a group of proteins in the nonreceptor tyrosine kinase (NRTKs) family, play a crucial role in growth, survival, and angiogenesis. They are activated by cytokines through the Janus kinase-signal transducer and activator of a transcription (JAK-STAT) signaling pathway. JAK-STAT signaling pathways have significant roles in the regulation of cell division, apoptosis, and immunity. Identification of the V617F mutation in the Janus homology 2 (JH2) domain of JAK2 leading to myeloproliferative disorders has stimulated great interest in the drug discovery community to develop JAK2-specific inhibitors. However, such inhibitors should be selective toward JAK2 over other JAKs and display an extended residence time. Recently, novel JAK2/STAT5 axis inhibitors (N-(1H-pyrazol-3-yl)pyrimidin-2-amino derivatives) have displayed extended residence times (hours or longer) on target and adequate selectivity excluding JAK3. To facilitate a deeper understanding of the kinase-inhibitor interactions and advance the development of such inhibitors, we utilize a multiscale Markovian milestoning with Voronoi tessellations (MMVT) approach within the Simulation-Enabled Estimation of Kinetic Rates v.2 (SEEKR2) program to rank order these inhibitors based on their kinetic properties and further explain the selectivity of JAK2 inhibitors over JAK3. Our approach investigates the kinetic and thermodynamic properties of JAK-inhibitor complexes in a user-friendly, fast, efficient, and accurate manner compared to other brute force and hybrid-enhanced sampling approaches.
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Affiliation(s)
- Anupam Anand Ojha
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Ambuj Srivastava
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Lane William Votapka
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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Roussey NM, Dickson A. Quality over quantity: Sampling high probability rare events with the weighted ensemble algorithm. J Comput Chem 2023; 44:935-947. [PMID: 36510846 PMCID: PMC10164457 DOI: 10.1002/jcc.27054] [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: 08/01/2022] [Revised: 10/27/2022] [Accepted: 11/27/2022] [Indexed: 12/15/2022]
Abstract
The prediction of (un)binding rates and free energies is of great significance to the drug design process. Although many enhanced sampling algorithms and approaches have been developed, there is not yet a reliable workflow to predict these quantities. Previously we have shown that free energies and transition rates can be calculated by directly simulating the binding and unbinding processes with our variant of the WE algorithm "Resampling of Ensembles by Variation Optimization", or "REVO". Here, we calculate binding free energies retrospectively for three SAMPL6 host-guest systems and prospectively for a SAMPL9 system to test a modification of REVO that restricts its cloning behavior in quasi-unbound states. Specifically, trajectories cannot clone if they meet a physical requirement that represents a high likelihood of unbinding, which in the case of this work is a center-of-mass to center-of-mass distance. The overall effect of this change was difficult to predict, as it results in fewer unbinding events each of which with a much higher statistical weight. For all four systems tested, this new strategy produced either more accurate unbinding free energies or more consistent results between simulations than the standard REVO algorithm. This approach is highly flexible, and any feature of interest for a system can be used to determine cloning eligibility. These findings thus constitute an important improvement in the calculation of transition rates and binding free energies with the weighted ensemble method.
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Affiliation(s)
- Nicole M Roussey
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Alex Dickson
- Department of Biochemistry and Molecular Biology, Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, Michigan, USA
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