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Thakkar R, Upreti D, Ishiguro S, Tamura M, Comer J. Computational design of a cyclic peptide that inhibits the CTLA4 immune checkpoint. RSC Med Chem 2023; 14:658-670. [PMID: 37122540 PMCID: PMC10131585 DOI: 10.1039/d2md00409g] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Proteins involved in immune checkpoint pathways, such as CTLA4, PD1, and PD-L1, have become important targets for cancer immunotherapy; however, development of small molecule drugs targeting these pathways has proven difficult due to the nature of their protein-protein interfaces. Here, using a hierarchy of computational techniques, we design a cyclic peptide that binds CTLA4 and follow this with experimental verification of binding and biological activity, using bio-layer interferometry, cell culture, and a mouse tumor model. Beginning from a template excised from the X-ray structure of the CTLA4:B7-2 complex, we generate several peptide sequences using flexible docking and modeling steps. These peptides are cyclized head-to-tail to improve structural and proteolytic stability and screened using molecular dynamics simulation and MM-GBSA calculation. The standard binding free energies for shortlisted peptides are then calculated in explicit-solvent simulation using a rigorous multistep technique. The most promising peptide, cyc(EIDTVLTPTGWVAKRYS), yields the standard free energy -6.6 ± 3.5 kcal mol-1, which corresponds to a dissociation constant of ∼15 μmol L-1. The binding affinity of this peptide for CTLA4 is measured experimentally (31 ± 4 μmol L-1) using bio-layer interferometry. Treatment with this peptide inhibited tumor growth in a co-culture of Lewis lung carcinoma (LLC) cells and antigen primed T cells, as well as in mice with an orthotropic Lewis lung carcinoma allograft model.
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Affiliation(s)
- Ravindra Thakkar
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
| | - Deepa Upreti
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
| | - Susumu Ishiguro
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
| | - Masaaki Tamura
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
| | - Jeffrey Comer
- Department of Anatomy and Physiology, Kansas State University 1620 Denison Avenue Manhattan Kansas USA +1 785 532 6311
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2
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Ochoa R, Cossio P, Fox T. Protocol for iterative optimization of modified peptides bound to protein targets. J Comput Aided Mol Des 2022; 36:825-835. [PMID: 36258137 PMCID: PMC9640467 DOI: 10.1007/s10822-022-00482-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/03/2022] [Indexed: 12/02/2022]
Abstract
Peptides are commonly used as therapeutic agents. However, they suffer from easy degradation and instability. Replacing natural by non-natural amino acids can avoid these problems, and potentially improve the affinity towards the target protein. Here, we present a computational pipeline to optimize peptides based on adding non-natural amino acids while improving their binding affinity. The workflow is an iterative computational evolution algorithm, inspired by the PARCE protocol, that performs single-point mutations on the peptide sequence using modules from the Rosetta framework. The modifications can be guided based on the structural properties or previous knowledge of the biological system. At each mutation step, the affinity to the protein is estimated by sampling the complex conformations and applying a consensus metric using various open protein-ligand scoring functions. The mutations are accepted based on the score differences, allowing for an iterative optimization of the initial peptide. The sampling/scoring scheme was benchmarked with a set of protein-peptide complexes where experimental affinity values have been reported. In addition, a basic application using a known protein-peptide complex is also provided. The structure- and dynamic-based approach allows users to optimize bound peptides, with the option to personalize the code for further applications. The protocol, called mPARCE, is available at: https://github.com/rochoa85/mPARCE/.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, 050010, Colombia. .,Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany.
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, 050010, Colombia.,Center for Computational Mathematics, Flatiron Institute, New York, 10010, USA.,Center for Computational Biology, Flatiron Institute, New York, 10010, USA
| | - Thomas Fox
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany
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3
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Zhou P, Wen L, Lin J, Mei L, Liu Q, Shang S, Li J, Shu J. Integrated unsupervised-supervised modeling and prediction of protein-peptide affinities at structural level. Brief Bioinform 2022; 23:6555404. [PMID: 35352094 DOI: 10.1093/bib/bbac097] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 12/24/2022] Open
Abstract
Cell signal networks are orchestrated directly or indirectly by various peptide-mediated protein-protein interactions, which are normally weak and transient and thus ideal for biological regulation and medicinal intervention. Here, we develop a general-purpose method for modeling and predicting the binding affinities of protein-peptide interactions (PpIs) at the structural level. The method is a hybrid strategy that employs an unsupervised approach to derive a layered PpI atom-residue interaction (ulPpI[a-r]) potential between different protein atom types and peptide residue types from thousands of solved PpI complex structures and then statistically correlates the potential descriptors with experimental affinities (KD values) over hundreds of known PpI samples in a supervised manner to create an integrated unsupervised-supervised PpI affinity (usPpIA) predictor. Although both the ulPpI[a-r] potential and usPpIA predictor can be used to calculate PpI affinities from their complex structures, the latter seems to perform much better than the former, suggesting that the unsupervised potential can be improved substantially with a further correction by supervised statistical learning. We examine the robustness and fault-tolerance of usPpIA predictor when applied to treat the coarse-grained PpI complex structures modeled computationally by sophisticated peptide docking and dynamics simulation. It is revealed that, despite developed solely based on solved structures, the integrated unsupervised-supervised method is also applicable for locally docked structures to reach a quantitative prediction but can only give a qualitative prediction on globally docked structures. The dynamics refinement seems not to change (or improve) the predictive results essentially, although it is computationally expensive and time-consuming relative to peptide docking. We also perform extrapolation of usPpIA predictor to the indirect affinity quantities of HLA-A*0201 binding epitope peptides and NHERF PDZ binding scaffold peptides, consequently resulting in a good and moderate correlation of the predicted KD with experimental IC50 and BLU on the two peptide sets, with Pearson's correlation coefficients Rp = 0.635 and 0.406, respectively.
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Affiliation(s)
- Peng Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu 611731, China
| | - Li Wen
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu 611731, China
| | - Jing Lin
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu 611731, China
| | - Li Mei
- Institute of Culinary, Sichuan Tourism University, Chengdu 610100, China
| | - Qian Liu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu 611731, China
| | - Shuyong Shang
- of Ecological Environment Protection, Chengdu Normal University, Chengdu 611130, China
| | - Juelin Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu 611731, China
| | - Jianping Shu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu 611731, China
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Guo Z, Liang E, Li W, Jiang L, Zhi F. Essential meiotic structure-specific endonuclease1 ( EME1) promotes malignant features in gastric cancer cells via the Akt/GSK3B/CCND1 pathway. Bioengineered 2021; 12:9869-9884. [PMID: 34719326 PMCID: PMC8810030 DOI: 10.1080/21655979.2021.1999371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
DNA damage plays a key role in various biological processes involved in malignant disease, the role of the DNA damage repair gene EME1 (essential meiotic structure-specific endonuclease 1) in gastric cancer (GC) development is unknown. This work aimed to investigate expression and role of EME1 in tumorigenesis. Quantitative real-time polymerase chain reaction (qRT-PCR), immunoblot, cell viability and dual-luciferase reporter assays, RNAi and gene transfection, and immunofluorescent staining were performed to assess EME1 regulation in GC tumorigenesis. Further, mouse xenografts were established for in vivo mechanistic studies. EME1 was found to be upregulated in both gastric cancer cells and clinically obtained tumors. Additionally, EME1 levels were strongly associated with the differentiation level of GC and lymph node metastasis. In vivo and in vitro knockdown of EME1 markedly suppressed the proliferative, migratory, and invasive abilities of GC cells and enhanced apoptotic cell death and cell cycle arrest rates. Mechanistically, EME1 modulated Akt/GSK3B/CCND1 signaling. MYB may also have contributed to EME1-dependent gastric carcinogenesis. Elevated EME1 expressions may enhance the proliferative and metastatic abilities of GC cells, thereby acting as a tumor-promoting factor via Akt. These findings reveal that EME1 is an important biomarker for GC prognosis and treatment in humans. Abbreviations: Essential meiotic structure-specific endonuclease 1 (EME1); MYB proto-oncogene (MYB); Cell counting kit-8 (CCK-8); 4,6-diamimo-2-phenyl indole (DAPI); Quantitative real-time PCR (qRT-PCR); Gastric cancer (GC); Immunofluorescence (IF); Small interfering RNA (siRNA); Small hairpin RNA (shRNA); Alpha serine threonine-protein kinase (Akt); Glycogen synthase kinase 3 beta (GSK3B); Cyclin D1 (CCND1); Glyceraldehyde-3-phosphate dehydrogenase (GAPDH); Disease-free survival (DFS); Overall survival (OS); Negative controls (NC); American Joint Committee on Cancer (AJCC); Coding sequence (CDS); Lymph node metastasis (LNM); Tris-Buffered Saline-Tween-20 (TBST); Horseradish Peroxidase (HRP); Electrochemiluminescence (ECL); Polyvinylidene Fluoride (PVDF); Excision repair cross complementation group 1 (ERCC1).
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Affiliation(s)
- Zhiguo Guo
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Erbo Liang
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Wei Li
- Department of Endocrinology, Suzhou Hospital of Anhui Medical University, Suzhou, Anhui 234000, China
| | - Leilei Jiang
- Department of Gastroenterology, Suzhou Hospital of Anhui Medical University, Suzhou, Anhui 234000, China
| | - Fachao Zhi
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
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Garofalo M, Grazioso G, Cavalli A, Sgrignani J. How Computational Chemistry and Drug Delivery Techniques Can Support the Development of New Anticancer Drugs. Molecules 2020; 25:E1756. [PMID: 32290224 PMCID: PMC7180704 DOI: 10.3390/molecules25071756] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/17/2023] Open
Abstract
The early and late development of new anticancer drugs, small molecules or peptides can be slowed down by some issues such as poor selectivity for the target or poor ADME properties. Computer-aided drug design (CADD) and target drug delivery (TDD) techniques, although apparently far from each other, are two research fields that can give a significant contribution to overcome these problems. Their combination may provide mechanistic understanding resulting in a synergy that makes possible the rational design of novel anticancer based therapies. Herein, we aim to discuss selected applications, some also from our research experience, in the fields of anticancer small organic drugs and peptides.
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Affiliation(s)
- Mariangela Garofalo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Giovanni Grazioso
- Department of Pharmaceutical Sciences, University of Milano, 20133 Milan, Italy
| | - Andrea Cavalli
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), 6500 Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), 6500 Bellinzona, Switzerland
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Diller DJ, Swanson J, Bayden AS, Brown CJ, Thean D, Lane DP, Partridge AW, Sawyer TK, Audie J. Rigorous Computational and Experimental Investigations on MDM2/MDMX-Targeted Linear and Macrocyclic Peptides. Molecules 2019; 24:E4586. [PMID: 31847417 PMCID: PMC6943714 DOI: 10.3390/molecules24244586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 12/25/2022] Open
Abstract
There is interest in peptide drug design, especially for targeting intracellular protein-protein interactions. Therefore, the experimental validation of a computational platform for enabling peptide drug design is of interest. Here, we describe our peptide drug design platform (CMDInventus) and demonstrate its use in modeling and predicting the structural and binding aspects of diverse peptides that interact with oncology targets MDM2/MDMX in comparison to both retrospective (pre-prediction) and prospective (post-prediction) data. In the retrospective study, CMDInventus modules (CMDpeptide, CMDboltzmann, CMDescore and CMDyscore) were used to accurately reproduce structural and binding data across multiple MDM2/MDMX data sets. In the prospective study, CMDescore, CMDyscore and CMDboltzmann were used to accurately predict binding affinities for an Ala-scan of the stapled α-helical peptide ATSP-7041. Remarkably, CMDboltzmann was used to accurately predict the results of a novel D-amino acid scan of ATSP-7041. Our investigations rigorously validate CMDInventus and support its utility for enabling peptide drug design.
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Affiliation(s)
- David J. Diller
- CMDBioscience, 5 Park Avenue, New Haven, CT 06511, USA; (D.J.D.); (J.S.); (A.S.B.)
- Venenum BioDesign, LLC, 8 Black Forest Road, Hamilton, NJ 08691, USA
| | - Jon Swanson
- CMDBioscience, 5 Park Avenue, New Haven, CT 06511, USA; (D.J.D.); (J.S.); (A.S.B.)
- ChemModeling, LLC, Suite 101, 500 Huber Park Ct, Weldon Spring, MO 63304, USA
| | - Alexander S. Bayden
- CMDBioscience, 5 Park Avenue, New Haven, CT 06511, USA; (D.J.D.); (J.S.); (A.S.B.)
- Kleo Pharmaceuticals, 25 Science Park, Ste 235, New Haven, CT 06511, USA
| | - Chris J. Brown
- A*STAR, p53 Laboratory, Singapore 138648, Singapore; (C.J.B.); (D.T.); (D.P.L.)
| | - Dawn Thean
- A*STAR, p53 Laboratory, Singapore 138648, Singapore; (C.J.B.); (D.T.); (D.P.L.)
| | - David P. Lane
- A*STAR, p53 Laboratory, Singapore 138648, Singapore; (C.J.B.); (D.T.); (D.P.L.)
| | - Anthony W. Partridge
- MSD International GmbH, Singapore 138665, Singapore;
- Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Tomi K. Sawyer
- Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Joseph Audie
- CMDBioscience, 5 Park Avenue, New Haven, CT 06511, USA; (D.J.D.); (J.S.); (A.S.B.)
- College of Arts and Sciences, Department of Chemistry, Sacred Heart University, 5151 Park Avenue, Fairfield, CT 06825, USA
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Strokach A, Corbi-Verge C, Kim PM. Predicting changes in protein stability caused by mutation using sequence-and structure-based methods in a CAGI5 blind challenge. Hum Mutat 2019; 40:1414-1423. [PMID: 31243847 PMCID: PMC6744338 DOI: 10.1002/humu.23852] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/16/2019] [Accepted: 06/24/2019] [Indexed: 12/26/2022]
Abstract
Predicting the impact of mutations on proteins remains an important problem. As part of the CAGI5 frataxin challenge, we evaluate the accuracy with which Provean, FoldX, and ELASPIC can predict changes in the Gibbs free energy of a protein using a limited data set of eight mutations. We find that different methods have distinct strengths and limitations, with no method being strictly superior to other methods on all metrics. ELASPIC achieves the highest accuracy while also providing a web interface which simplifies the evaluation and analysis of mutations. FoldX is slightly less accurate than ELASPIC but is easier to run locally, as it does not depend on external tools or datasets. Provean achieves reasonable results while being computational less expensive than the other methods and not requiring a structure of the protein. In addition to methods submitted to the CAGI5 community experiment, and with the aim to inform about other methods with high accuracy, we also evaluate predictions made by Rosetta's ddg_monomer protocol, Rosetta's cartesian_ddg protocol, and thermodynamic integration calculations using Amber package. ELASPIC still achieves the highest accuracy, while Rosetta's catesian_ddg protocol appears to perform best in capturing the overall trend in the data.
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Affiliation(s)
- Alexey Strokach
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Carles Corbi-Verge
- Donnelly Centre for Cellular and Biomolecular Research, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Philip M Kim
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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