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Sobhani N, Tardiel-Cyril DR, Chai D, Generali D, Li JR, Vazquez-Perez J, Lim JM, Morris R, Bullock ZN, Davtyan A, Cheng C, Decker WK, Li Y. Artificial intelligence-powered discovery of small molecules inhibiting CTLA-4 in cancer. BJC REPORTS 2024; 2:4. [PMID: 38312352 PMCID: PMC10838660 DOI: 10.1038/s44276-023-00035-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 12/14/2023] [Accepted: 12/28/2023] [Indexed: 02/06/2024]
Abstract
BACKGROUND/OBJECTIVES Checkpoint inhibitors, which generate durable responses in many cancer patients, have revolutionized cancer immunotherapy. However, their therapeutic efficacy is limited, and immune-related adverse events are severe, especially for monoclonal antibody treatment directed against cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), which plays a pivotal role in preventing autoimmunity and fostering anticancer immunity by interacting with the B7 proteins CD80 and CD86. Small molecules impairing the CTLA-4/CD80 interaction have been developed; however, they directly target CD80, not CTLA-4. SUBJECTS/METHODS In this study, we performed artificial intelligence (AI)-powered virtual screening of approximately ten million compounds to identify those targeting CTLA-4. We validated the hits molecules with biochemical, biophysical, immunological, and experimental animal assays. RESULTS The primary hits obtained from the virtual screening were successfully validated in vitro and in vivo. We then optimized lead compounds and obtained inhibitors (inhibitory concentration, 1 micromole) that disrupted the CTLA-4/CD80 interaction without degrading CTLA-4. CONCLUSIONS Several compounds inhibited tumor development prophylactically and therapeutically in syngeneic and CTLA-4-humanized mice. Our findings support using AI-based frameworks to design small molecules targeting immune checkpoints for cancer therapy.
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Affiliation(s)
- Navid Sobhani
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | | | - Dafei Chai
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniele Generali
- Department of Medical, Surgery and Health Sciences, University of Trieste, 34147 Trieste, Italy
| | - Jian-Rong Li
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan Vazquez-Perez
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jing Ming Lim
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rachel Morris
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Zaniqua N. Bullock
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aram Davtyan
- Atomwise Inc., 717 Market St, Suite 800, San Francisco, CA 94103, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - William K. Decker
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yong Li
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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Bojadzic D, Buchwald P. Toward Small-Molecule Inhibition of Protein-Protein Interactions: General Aspects and Recent Progress in Targeting Costimulatory and Coinhibitory (Immune Checkpoint) Interactions. Curr Top Med Chem 2018; 18:674-699. [PMID: 29848279 PMCID: PMC6067980 DOI: 10.2174/1568026618666180531092503] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/27/2018] [Accepted: 05/11/2018] [Indexed: 02/06/2023]
Abstract
Protein-Protein Interactions (PPIs) that are part of the costimulatory and coinhibitory (immune checkpoint) signaling are critical for adequate T cell response and are important therapeutic targets for immunomodulation. Biologics targeting them have already achieved considerable clinical success in the treatment of autoimmune diseases or transplant recipients (e.g., abatacept, belatacept, and belimumab) as well as cancer (e.g., ipilimumab, nivolumab, pembrolizumab, atezolizumab, durvalumab, and avelumab). In view of such progress, there have been only relatively limited efforts toward developing small-molecule PPI inhibitors (SMPPIIs) targeting these cosignaling interactions, possibly because they, as all other PPIs, are difficult to target by small molecules and were not considered druggable. Nevertheless, substantial progress has been achieved during the last decade. SMPPIIs proving the feasibility of such approaches have been identified through various strategies for a number of cosignaling interactions including CD40-CD40L, OX40-OX40L, BAFFR-BAFF, CD80-CD28, and PD-1-PD-L1s. Here, after an overview of the general aspects and challenges of SMPPII-focused drug discovery, we review them briefly together with relevant structural, immune-signaling, physicochemical, and medicinal chemistry aspects. While so far only a few of these SMPPIIs have shown activity in animal models (DRI-C21045 for CD40-D40L, KR33426 for BAFFR-BAFF) or reached clinical development (RhuDex for CD80-CD28, CA-170 for PD-1-PD-L1), there is proof-of-principle evidence for the feasibility of such approaches in immunomodulation. They can result in products that are easier to develop/ manufacture and are less likely to be immunogenic or encounter postmarket safety events than corresponding biologics, and, contrary to them, can even become orally bioavailable.
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Affiliation(s)
- Damir Bojadzic
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Peter Buchwald
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, Florida, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, USA
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Lotfi-Emran S, Ward BR, Le QT, Pozez AL, Manjili MH, Woodfolk JA, Schwartz LB. Human mast cells present antigen to autologous CD4 + T cells. J Allergy Clin Immunol 2017. [PMID: 28624612 DOI: 10.1016/j.jaci.2017.02.048] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Mast cells (MCs), the primary effector cell of the atopic response, participate in immune defense at host/environment interfaces, yet the mechanisms by which they interact with CD4+ T cells has been controversial. OBJECTIVE We used in situ-matured primary human MCs and matched CD4+ T cells to diligently assess the ability of MCs to act as antigen-presenting cells. METHODS We examined mature human skin-derived MCs using flow cytometry for expression of antigen-presenting molecules, for their ability to stimulate CD4+ T cells to express CD25 and proliferate when exposed to superantigen or to cytomegalovirus (CMV) antigen using matched T cells and MCs from CMV-seropositive or CMV-seronegative donors, and for antigen uptake. Subcellular localization of antigen, HLA molecules, and tryptase was analyzed by using structured illumination microscopy. RESULTS Our data show that IFN-γ induces HLA class II, HLA-DM, CD80, and CD40 expression on MCs, whereas MCs take up soluble and particulate antigens in an IFN-γ-independent manner. IFN-γ-primed MCs guide activation of T cells by Staphylococcus aureus superantigen and, when preincubated with CMV antigens, induce a recall CD4+ TH1 proliferation response only in CMV-seropositive donors. MCs co-opt their secretory granules for antigen processing and presentation. Consequently, MC degranulation increases surface delivery of HLA class II/peptide, further enhancing stimulation of T-cell proliferation. CONCLUSIONS IFN-γ primes human MCs to activate T cells through superantigen and to present CMV antigen to TH1 cells, co-opting MC secretory granules for antigen processing and presentation and creating a feed-forward loop of T-cell-MC cross-activation.
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Affiliation(s)
- Sahar Lotfi-Emran
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Va
| | - Brant R Ward
- Division of Rheumatology, Allergy and Immunology, Virginia Commonwealth University, Richmond, Va
| | - Quang T Le
- Division of Rheumatology, Allergy and Immunology, Virginia Commonwealth University, Richmond, Va
| | - Andrea L Pozez
- Division of Plastic and Reconstructive Surgery, Virginia Commonwealth University, Richmond, Va
| | - Masoud H Manjili
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Va; Massey Cancer Center, Virginia Commonwealth University, Richmond, Va
| | - Judith A Woodfolk
- Division of Asthma, Allergy, and Immunology, University of Virginia, Charlottesville, Va
| | - Lawrence B Schwartz
- Division of Rheumatology, Allergy and Immunology, Virginia Commonwealth University, Richmond, Va.
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Zarzycka B, Nicolaes GAF, Lutgens E. Targeting the adaptive immune system: new strategies in the treatment of atherosclerosis. Expert Rev Clin Pharmacol 2015; 8:297-313. [PMID: 25843158 DOI: 10.1586/17512433.2015.1025052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Atherosclerosis is a lipid-driven chronic inflammatory disease of the arterial wall. Current treatment of atherosclerosis is focused on limiting its risk factors, such as hyperlipidemia or hypertension. However, treatments that target the inflammatory nature of atherosclerosis are still under development. Discovery of novel targets involved in the inflammation of the arterial wall creates opportunities to design new therapeutics that successfully modulate atherosclerosis. Here, we review drug targets that have proven to play pivotal roles in the adaptive immune system in atherosclerosis, and we discuss their potential as novel therapeutics.
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Affiliation(s)
- Barbara Zarzycka
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD Maastricht, The Netherlands
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García-Hernández MH, González-Amaro R, Portales-Pérez DP. Specific therapy to regulate inflammation in rheumatoid arthritis: molecular aspects. Immunotherapy 2015; 6:623-36. [PMID: 24896630 DOI: 10.2217/imt.14.26] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disease in which persistent inflammation of synovial tissue results in a progressive functional decline of the joint and premature mortality. TNF inhibitors were the first biological disease-modifying antirheumatic drugs (DMARDs) used to treat RA. Since then, new biological drugs have emerged, such as inhibitors of IL-1, IL-6 and others, with different mechanisms of action that include the depletion of B cells and the inhibition of T-cell costimulation. Recently, RA treatments have incorporated the use of synthetic DMARDs. This review describes the molecular aspects of the mechanisms of action of biological and synthetic DMARDs, discusses the adverse effects and limitations of established therapies and analyses the alternative approaches to RA treatment.
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Affiliation(s)
- Mariana H García-Hernández
- Laboratory of Immunology & Cellular & Molecular Biology, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, SLP, México
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Heninger AK, Wentrup S, Al-Saeedi M, Schiessling S, Giese T, Wartha F, Meuer S, Schröder-Braunstein J. Immunomodulation of human intestinal T cells by the synthetic CD80 antagonist RhuDex®. IMMUNITY INFLAMMATION AND DISEASE 2014; 2:166-80. [PMID: 25505551 PMCID: PMC4257762 DOI: 10.1002/iid3.34] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 08/13/2014] [Accepted: 08/25/2014] [Indexed: 12/17/2022]
Abstract
Deregulated activation of mucosal lamina propria T cells plays a central role in the pathogenesis of intestinal inflammation. One of the means to attenuate T cell activation is by blocking the CD28/CD80 co-stimulatory pathway. Here we investigate RhuDex®, a small molecule that binds to human CD80, for its effects on the activation of lamina propria T cells employing a gut-culture model of inflammation. To this end, lamina propria leukocytes (LPL) and peripheral blood lymphocytes (PBL) were stimulated either through the CD3/T-cell-receptor complex or the CD2-receptor (CD2) employing agonistic monoclonal antibodies. Co-stimulatory signals were provided by CD80/CD86 present on lamina propria myeloid cells or LPS-activated peripheral blood monocytes. Results show that RhuDex® caused a profound reduction of LPL and PBL proliferation, while Abatacept (CTLA-4-Ig) inhibited LPL proliferation to a small degree, and had no effect on PBL proliferation. Furthermore, Abatacept significantly inhibited IL-2, TNF-α, and IFN-γ release from LPL, primarily produced by CD4+ T cells, where IL-2 blockage was surprisingly strong, suggesting a down-regulating effect on regulatory T cells. In contrast, in the presence of RhuDex®, secretion of IL-17, again mostly by CD4+ T cells, and IFN-γ was inhibited in LPL and PBL, yet IL-2 remained unaffected. Thus, RhuDex® efficiently inhibited lamina propria and peripheral blood T-cell activation in this pre-clinical study making it a promising drug candidate for the treatment of intestinal inflammation.
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Affiliation(s)
- Anne-Kristin Heninger
- Institute for Immunology, University Hospital Heidelberg Im Neuenheimer Feld 305, 69120, Heidelberg, Germany
| | - Sabine Wentrup
- Institute for Immunology, University Hospital Heidelberg Im Neuenheimer Feld 305, 69120, Heidelberg, Germany
| | - Mohammed Al-Saeedi
- Department of General, Visceral and Transplant Surgery, University Hospital Heidelberg Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Serin Schiessling
- Institute for Immunology, University Hospital Heidelberg Im Neuenheimer Feld 305, 69120, Heidelberg, Germany ; Department of General, Visceral and Transplant Surgery, University Hospital Heidelberg Im Neuenheimer Feld 110, 69120, Heidelberg, Germany
| | - Thomas Giese
- Institute for Immunology, University Hospital Heidelberg Im Neuenheimer Feld 305, 69120, Heidelberg, Germany
| | - Florian Wartha
- Medigene AG Lochhamer Str. 11, 82152, Planegg/Martinsried, Germany
| | - Stefan Meuer
- Institute for Immunology, University Hospital Heidelberg Im Neuenheimer Feld 305, 69120, Heidelberg, Germany
| | - Jutta Schröder-Braunstein
- Institute for Immunology, University Hospital Heidelberg Im Neuenheimer Feld 305, 69120, Heidelberg, Germany
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Doesch AO, Zhao L, Gleissner CA, Akhavanpoor M, Rohde D, Okuyucu D, Hakimi M, Dengler TJ, Katus HA, Erbel C. Inhibition of B7-1 (CD80) by RhuDex® reduces lipopolysaccharide-mediated inflammation in human atherosclerotic lesions. DRUG DESIGN DEVELOPMENT AND THERAPY 2014; 8:447-57. [PMID: 24872677 PMCID: PMC4026407 DOI: 10.2147/dddt.s59594] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Background Atherosclerosis is based on a chronic inflammatory process including the innate and adaptive immune response. Costimulatory molecules and their receptors provide decisive signals for antigen-specific cell activation. The contribution of B7-related pathways to atherosclerosis has hardly been explored. Methods In the present study, we investigated the contribution of B7-1 to inflammation and tissue injury in the human plaque microenvironment in order to identify possible target structures of future therapeutic agents ex vivo and in vitro. Results Carotid artery plaque stimulation with lipopolysaccharides (LPS) could be significantly inhibited by RhuDex®, a specific inhibitor of the costimulatory molecule B7-1 ex vivo (P<0.001). Coculture of antigen-presenting cells with T-cells demonstrated that the inhibitory effects of RhuDex® derived from reduced T-cell activation. In addition, incubation of monocytes/macrophages with LPS and RhuDex® resulted in an inhibitory negative feedback on antigen-presenting cells. Signaling pathways affected by RhuDex® seem to be nuclear transcription factor kappa B, activator protein-1, and extracellular signal-regulated kinase 1/2. Conclusion The present data support B7-1 alone as an important costimulatory molecule in the context of LPS-mediated inflammation in atherosclerotic lesions. Due to its marked inhibitory effects, RhuDex® may be a useful therapy to modulate the inflammatory milieu in atherosclerosis.
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Affiliation(s)
| | - Li Zhao
- Department of Cardiology, University of Heidelberg, Germany
| | | | | | - David Rohde
- Department of Cardiology, University of Heidelberg, Germany
| | - Deniz Okuyucu
- Department of Cardiology, University of Heidelberg, Germany
| | - Maani Hakimi
- Department of Vascular Surgery, University of Heidelberg, Germany
| | - Thomas J Dengler
- Department of Cardiology, SLK Hospital Heilbronn, Bad Friedrichshall, Germany
| | - Hugo A Katus
- Department of Cardiology, University of Heidelberg, Germany
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Jonker M, Wubben J, Haanstra K, Vierboom M, 't Hart B. Comparative analysis of inflammatory infiltrates in collagen-induced arthritis, kidney graft rejection and delayed-type hypersensitivity in non-human primates. Inflamm Res 2012; 62:181-94. [PMID: 23064655 DOI: 10.1007/s00011-012-0564-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 08/15/2012] [Accepted: 10/03/2012] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES Non-human primates are immunologically closely related to humans providing relevant models of inflammatory disorders often used to evaluate new immunomodulating therapies. The aim of the study was to compare inflammatory infiltrates of acute graft rejection (AR) and collagen-induced arthritis (CIA) to delayed-type hypersensitivity (DTH) reactions as the latter model may serve as a less invasive animal model. MATERIALS AND METHODS Tissue samples of AR, CIA and DTH were obtained from rhesus monkeys used in several pre-clinical studies. The infiltrate composition was determined by immunohistochemical analysis. RESULTS The infiltrates in AR consisted of T cells, macrophages and B cells. The presence of lymphoid structures in AR suggested ongoing intragraft immune activation. The synovia of CIA contained predominantly macrophages and few T cells. The DTH infiltrates were dominated by T cells when the challenged was ovalbumin (OVA) and by macrophages when the challenge was tetanus toxoid (TT). CONCLUSIONS The histology of AR resembles aspects of DTH to OVA while that of CIA showed similarities of the DTH to TT. The DTH reaction could serve as a model to study immunomodulating drugs for acute rejection and the acute inflammatory phase of autoimmunity.
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Affiliation(s)
- Margreet Jonker
- Biomedical Primate Research Centre, PO BOX 3306, 2280 GH Rijswijk, Netherlands.
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Shi Q, Gao ZY, Xie F, Wang LF, Gu YP, Yang TJ, Huang L, Qian QH, Qiu YH. A novel monoclonal antibody against human CD80 and its immune protection in a mouse lupus-like disease. Int J Immunopathol Pharmacol 2011; 24:583-93. [PMID: 21978690 DOI: 10.1177/039463201102400304] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Blockade of the interactions between CD28/CTLA-4 and their ligands, CD80 (B7, B7.1)/CD86 (B70, B7.2), is an attractive means to induce antigen-specific peripheral tolerance in autoimmune disease and organ transplantation. In this study, we generated and characterized a monoclonal antibody (Clone 4E5) against human CD80. 4E5 could recognize both human and mouse CD80 and suppress mixed lymphocyte reaction in vitro. To investigate their potency for clinical use, we further administrated 4E5 to a mouse lupus-like disease model (C57BL/J6) induced by Pristane. 4E5 could inhibit the immune response and attenuate the severity of lupus-like disease. The data showed 4E5 function and suggested that blockade of CD80/CD28 co-stimulatory signal pathway with 4E5 is a promising strategy to decelerate the progression of lupus-like disease and other autoimmune diseases.
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Affiliation(s)
- Q Shi
- Orthopedic Department, First Affiliated Hospital of Soochow University, Suzhou, China
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