Drug Discovery Biology Research Articles

Structural Biology in Drug Discovery and Development: Call for Papers

Structural Biology in Drug Discovery and Development: Call for Papers

TAC-tics for Leveraging Proximity Biology in Drug Discovery.

Chemically induced proximity (CIP) refers to co-opting naturally occurring biological pathways using synthetic molecules to recruit neosubstrates that are not normally encountered or to enhance the affinity of naturally occurring interactions. Leveraging proximity biology through CIPs has become a rapidly evolving field and has garnered considerable interest in basic research and drug discovery. PROteolysis TArgeting Chimera (PROTAC) is a well-established CIP modality that induces the proximity between a target protein and an E3 ubiquitin ligase, causing target protein degradation via the ubiquitin-proteasome system. Inspired by PROTACs, several other induced proximity modalities have emerged to modulate both proteins and RNA over recent years. In this review, we summarize the critical advances and opportunities in the field, focusing on protein degraders, RNA degraders and non-degrader modalities such as post-translational modification (PTM) and protein-protein interaction (PPI) modulators. We envision that these emerging proximity-based drug modalities will be valuable resources for both biological research and therapeutic discovery in the future.

Applications of synthetic biology in drug discovery

Applications of synthetic biology in drug discovery

Translatability of In Vitro Stress for Predicting Deamidation and Oxidation Biotransformation on Biotherapeutics.

Biotransformation leading to single residue modifications (e.g., deamidation, oxidation) can contribute to decreased efficacy/potency, poor pharmacokinetics, and/or toxicity/immunogenicity for protein therapeutics. Identifying and characterizing such liabilities in vivo are emerging needs for biologics drug discovery. In vitro stress assays involving PBS for deamidation or AAPH for oxidation are commonly used for predicting liabilities in manufacturing and storage and are sometimes considered a predictive tool for in vivo liabilities. However, reports discussing their in vivo translatability are limited. Herein, we introduce a mass spectrometry workflow that characterizes in vivo oxidation and deamidation in pharmacokinetically relevant compartments for diverse protein therapeutic modalities. The workflow has low bias of <10% in quantitating degradation in the relevant pharmacokinetic concentration range for monkey and rabbit serum/plasma (1-100 μg/mL) and allows for high sequence coverage (∼85%) for discovery/monitoring of amino acid modifications. For oxidation and deamidation, the assay was precise, with percent coefficient of variation of <8% at 1-100 μg/mL and ≤6% method-induced artifacts. A high degree of in vitro and in vivo correlation was observed for deamidation on the six diverse protein therapeutics (seven liability sites) tested. In vivo translatability for oxidation liabilities were not observed for the 11 molecules tested using in vitro AAPH stress. One of the molecules dosed in eyes resulted in a false positive and a false negative prediction for in vivo oxidation following AAPH stress. Finally, peroxide stress was also tested but resulted in limited success (1 out of 4 molecules) in predicting oxidation liabilities.

Abstract 1537: DRIVE-Biologics: All the steps from discovery to development of novel biological entities

Abstract Biologics first revolutionized cancer treatment in the late 1900s with the approval of rituximab and trastuzumab, two monoclonal antibodies targeting antigens expressed on tumor cells. Another milestone was achieved in the early 2010s with the approval of antibodies targeting immune checkpoints. Nowadays, the discovery and development of new biological entities and biological therapeutic products represent a rapidly growing market in various therapeutic areas, with about 10 to 15 biologics being approved each year. We have built a premium expert ecosystem services - DRIVE-Biologics - to support and accelerate biologics drug discovery and development in oncology, immuno-oncology, and inflammatory diseases. The DRIVE-Biologics consortium provides a unique integrated solution with specialist services from strategic partners, to access market analysis, establish the ability to design, optimize, and develop novel biological entities addressing the therapeutic target of interest. DRIVE-Biologics supplies the high-level, IND-focused discipline to rigorously manage the integrated programs integrating CMC, manufacturing, regulatory affairs and clinical trial. We will present the lead optimization and multiparameter preclinical evaluation process to select and assess biological candidates for downstream development and clinical studies: -Custom cellular model development for discovery and potency analysis; -In vitro screening, target engagement, and mechanism of action elucidation with cellular models ranging from tumor cell lines, immune cells or primary patient samples; -In vivo efficacy and safety studies using refined and highly characterized syngeneic, xenogeneic, patient-derived xenograft or humanized mouse models up to non-human primates; -DMPK capabilities to develop and validate bioanalytical methods (including GLP-compliancy) such as LBA and qPCR/RT-qPCR and also assess immunogenicity; -Biodistribution and tumor specificity analysis of bioconjugated and radiolabeled biologics. Herein, we provide DRIVE-BIO optimization and preclinical evaluation process to select promising biologics and list the key parameters to be checked. We will present our recent results which highlight the importance to optimize these parameters to improve the efficacy of biologics. Citation Format: Emily Fang, Campbell Bunce, Philip Payne, Rafael Teran, Olivier Duchamp, Caroline Mignard, Francis Bichat, Fabrice Viviani. DRIVE-Biologics: All the steps from discovery to development of novel biological entities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1537.

Predictive modelling and simulation for taming the chance and luck in biologics drug discovery

Predictive modelling and simulation for taming the chance and luck in biologics drug discovery

Crossing the Valley of Death: The Effect of Organizational Form and Technology Age on Exploration

In this article, we study the effect of organizational form (i.e., universities, entrants, and incumbents), technology age, and prior failure in the technology class on the success in exploring new technology. Utilizing data from over 7000 biological drug discovery projects over a 30-year period, we model the likelihood that a drug discovery project will be carried over to a Phase 1 clinical trial. We find that, despite early and pioneering success, projects by universities and specialist biotech companies are less likely to succeed as technology ages, while the likelihood of big pharma projects succeeding increases. Moreover, prior failure in the technology class has a detrimental impact on the likelihood of success of projects originated by biotech companies and universities while big pharma’s projects remain relatively undeterred by these failures. We argue that, contrary to the recent literature, these findings suggest that the exploration by large established organizations remains important to the innovation process and, consequently, they should remain active in exploration. In the article, we explain the mechanisms underpinning these empirical findings and clarify why our findings on the role of different organizational forms in exploration seemingly contradict the recent literature on innovation.

Enhancing preclinical predictivity in I-O: what is going wrong between preclinical in vitro/in vivo and clinical settings?

Enhancing preclinical predictivity in I-O: what is going wrong between preclinical in vitro/in vivo and clinical settings?

A Perspective on Synthetic Biology in Drug Discovery and Development—Current Impact and Future Opportunities

The global impact of synthetic biology has been accelerating, because of the plummeting cost of DNA synthesis, advances in genetic engineering, growing understanding of genome organization, and explosion in data science. However, much of the discipline’s application in the pharmaceutical industry remains enigmatic. In this review, we highlight recent examples of the impact of synthetic biology on target validation, assay development, hit finding, lead optimization, and chemical synthesis, through to the development of cellular therapeutics. We also highlight the availability of tools and technologies driving the discipline. Synthetic biology is certainly impacting all stages of drug discovery and development, and the recognition of the discipline’s contribution can further enhance the opportunities for the drug discovery and development value chain.

Potency-Enhancing Mutations of Gating Modifier Toxins for the Voltage-Gated Sodium Channel NaV1.7 Can Be Predicted Using Accurate Free-Energy Calculations.

Gating modifier toxins (GMTs) isolated from venomous organisms such as Protoxin-II (ProTx-II) and Huwentoxin-IV (HwTx-IV) that inhibit the voltage-gated sodium channel NaV1.7 by binding to its voltage-sensing domain II (VSDII) have been extensively investigated as non-opioid analgesics. However, reliably predicting how a mutation to a GMT will affect its potency for NaV1.7 has been challenging. Here, we hypothesize that structure-based computational methods can be used to predict such changes. We employ free-energy perturbation (FEP), a physics-based simulation method for predicting the relative binding free energy (RBFE) between molecules, and the cryo electron microscopy (cryo-EM) structures of ProTx-II and HwTx-IV bound to VSDII of NaV1.7 to re-predict the relative potencies of forty-seven point mutants of these GMTs for NaV1.7. First, FEP predicted these relative potencies with an overall root mean square error (RMSE) of 1.0 ± 0.1 kcal/mol and an R2 value of 0.66, equivalent to experimental uncertainty and an improvement over the widely used molecular-mechanics/generalized born-surface area (MM-GB/SA) RBFE method that had an RMSE of 3.9 ± 0.8 kcal/mol. Second, inclusion of an explicit membrane model was needed for the GMTs to maintain stable binding poses during the FEP simulations. Third, MM-GB/SA and FEP were used to identify fifteen non-standard tryptophan mutants at ProTx-II[W24] predicted in silico to have a at least a 1 kcal/mol gain in potency. These predicted potency gains are likely due to the displacement of high-energy waters as identified by the WaterMap algorithm for calculating the positions and thermodynamic properties of water molecules in protein binding sites. Our results expand the domain of applicability of FEP and set the stage for its prospective use in biologics drug discovery programs involving GMTs and NaV1.7.

A custom ÄKTA avant configuration enabling automated parallel protein purification over a range of process scales

Biologics are making up an increasing proportion of the global drug discovery pipeline. Supporting the expansion of biologics drug discovery requires higher throughput techniques for the expression, purification and characterization of both therapeutic candidates and reagents. Here we describe the programming and development of a novel ÄKTA™ instrument configuration that enables automated parallel and multistep chromatography over a range of scales. The programming strategy is offered as open source and the custom plumbing configuration was developed with off the shelf components available from Cytiva. Combined with high flow resin technology we show how this strategy can reduce the duration of a standard antibody purification process by 4.5X, from 4.5 h down to 1 h per run. An automated loading strategy was also developed to enable true walk away application of up to 24 samples and around the clock processing capability. The techniques used here to accomplish parallel multistep chromatography can be duplicated or modified for specific applications and represent a straightforward and cost-effective means to eliminate protein purification bottlenecks.

Abstract 944: Quantitative cell-based reporter bioassays for functional characterization of immunotherapeutic biologics targeting co-stimulatory and co-inhibitory immune checkpoint receptors

Abstract The human immune system is regulated by a complex network of inhibitory and stimulatory immune checkpoint receptors that regulate T Cell function. These receptors are promising new immunotherapy targets for the treatment of a variety of cancers and autoimmune disorders. Novel therapies employing a variety of strategies have been developed that rely on releasing the brakes on the immune system, with the aim of eliminating tumor cells even more efficiently. Immunotherapies designed to block co-inhibitory receptors (e.g. PD-1, CTLA-4) are showing unprecedented efficacy in the treatment of cancer. However, not all patients and tumor types respond to this approach. This has resulted in broadening of immunotherapy research programs to target additional co-inhibitory (e.g. LAG-3, TIM-3, TIGIT) and co-stimulatory (e.g. 4-1BB, GITR, OX40, ICOS) receptors, individually and in combination. A major challenge in the development of antibody-based biologics is access to quantitative and reproducible functional bioassays. Existing methods rely on primary cells and measurement of complex functional endpoints. These assays are cumbersome, highly variable and fail to yield data required for drug development in a quality-controlled environment. To address this need, we have developed a suite of cell-based functional bioassays to interrogate modulation of immune checkpoint receptors individually (e.g. PD-1, LAG-3, TIM-3, GITR, 4-1BB) and in combination (e.g. PD-1+CTLA-4, PD-1+LAG-3). These bioassays consist of stable cell lines that express luciferase reporters driven by response elements under the precise control of mechanistically relevant intracellular signals from TCR and immune checkpoint receptors. Thus, these bioassays reflect mechanisms of action for drug candidates designed for each immune checkpoint receptor and demonstrate high specificity, sensitivity and reproducibility. The bioassays are prequalified according to ICH guidelines and show the precision, accuracy and linearity required for routine use in potency and stability studies. Here we describe the application of MoA-based immune checkpoint receptor bioassays as tools for biologics drug discovery, development, potency and stability studies. Citation Format: Jamison Grailer, Julia Gilden, Pete Stecha, Denise Garvin, Jun Wang, Michael Beck, Jim Hartnett, Gopal Krishnan, Frank Fan, Mei Cong, Zhi-jie Jey Cheng. Quantitative cell-based reporter bioassays for functional characterization of immunotherapeutic biologics targeting co-stimulatory and co-inhibitory immune checkpoint receptors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 944.

Mechanisms of Action for Small Molecules Revealed by Structural Biology in Drug Discovery.

Small-molecule drugs are organic compounds affecting molecular pathways by targeting important proteins. These compounds have a low molecular weight, making them penetrate cells easily. Small-molecule drugs can be developed from leads derived from rational drug design or isolated from natural resources. A target-based drug discovery project usually includes target identification, target validation, hit identification, hit to lead and lead optimization. Understanding molecular interactions between small molecules and their targets is critical in drug discovery. Although many biophysical and biochemical methods are able to elucidate molecular interactions of small molecules with their targets, structural biology is the most powerful tool to determine the mechanisms of action for both targets and the developed compounds. Herein, we reviewed the application of structural biology to investigate binding modes of orthosteric and allosteric inhibitors. It is exemplified that structural biology provides a clear view of the binding modes of protease inhibitors and phosphatase inhibitors. We also demonstrate that structural biology provides insights into the function of a target and identifies a druggable site for rational drug design.

Recent Advances in System Based Study for Anti-Malarial Drug Development Process

Presently, malaria is one of the most prevalent and deadly infectious disease across Africa, Asia, and America that has now started to spread in Europe. Despite large research being carried out in the field, still, there is a lack of efficient anti-malarial therapeutics. In this paper, we highlight the increasing efforts that are urgently needed towards the development and discovery of potential antimalarial drugs, which must be safe and affordable. The new drugs thus mentioned are also able to counter the spread of malaria parasites that have been resistant to the existing agents. The main objective of the review is to highlight the recent development in the use of system biologybased approaches towards the design and discovery of novel anti-malarial inhibitors. A huge literature survey was performed to gain advance knowledge about the global persistence of malaria, its available treatment and shortcomings of the available inhibitors. Literature search and depth analysis were also done to gain insight into the use of system biology in drug discovery and how this approach could be utilized towards the development of the novel anti-malarial drug. The system-based analysis has made easy to understand large scale sequencing data, find candidate genes expression during malaria disease progression further design of drug molecules those are complementary of the target proteins in term of shape and configuration. The review article focused on the recent computational advances in new generation sequencing, molecular modeling, and docking related to malaria disease and utilization of the modern system and network biology approach to antimalarial potential drug discovery and development.

Abstract 4113: Quantitative cell-based bioassays to advance immunotherapy programs targeting immune checkpoint receptors

Abstract The human immune system is comprised of a complex network of immune checkpoint receptors that are promising new immunotherapy targets for the treatment of a variety of cancers and autoimmune disorders. The Nobel prize for Medicine in 2018 was awarded for seminal studies on the role of immune checkpoint targets in T cell activation and furthermore, combining different strategies to release the brakes on the immune system with the aim of eliminating tumor cells even more efficiently. Immunotherapies designed to block co-inhibitory receptors (e.g. PD-1, CTLA-4, TIGIT) are showing unprecedented efficacy in the treatment of cancer. However, not all patients and tumor types respond to this approach. This has resulted in broadening of immunotherapy research programs to target additional co-inhibitory (e.g. LAG-3, TIM-3) and co-stimulatory (e.g. 4-1BB, GITR, OX40, ICOS) receptors individually and in combination. A major challenge in the development of antibody-based biologics is access to quantitative and reproducible functional bioassays. Existing methods rely on primary cells and measurement of complex functional endpoints. These assays are cumbersome, highly variable and fail to yield data required for drug development in a quality-controlled environment. To address this need, we have developed a suite of cell-based functional bioassays to interrogate modulation of immune checkpoint receptors individually (e.g. PD-1, LAG-3, TIM-3, GITR, 4-1BB) and in combination (e.g. PD-1+CTLA-4, PD-1+LAG-3). These assays consist of stable cell lines that express luciferase reporters driven by response elements under the precise control of mechanistically relevant intracellular signals. Thus, the bioassays reflect mechanisms of action for the drug candidates designed for each immune checkpoint receptor and demonstrate high specificity, sensitivity and reproducibility. Here we describe the application of MoA-based immune checkpoint receptor bioassays as tools for biologics drug discovery, development, potency and stability studies. Citation Format: Jamison Grailer, Julia Gilden, Pete Stecha, Denise Garvin, Jun Wang, Michael Beck, Jim Hartnett, Gopal Krishnan, Frank Fan, Mei Cong, Zhi-jie Jey Cheng. Quantitative cell-based bioassays to advance immunotherapy programs targeting immune checkpoint receptors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4113.

Nanoscale integration of single cell biologics discovery processes using optofluidic manipulation and monitoring.

The new and rapid advancement in the complexity of biologics drug discovery has been driven by a deeper understanding of biological systems combined with innovative new therapeutic modalities, paving the way to breakthrough therapies for previously intractable diseases. These exciting times in biomedical innovation require the development of novel technologies to facilitate the sophisticated, multifaceted, high‐paced workflows necessary to support modern large molecule drug discovery. A high‐level aspiration is a true integration of “lab‐on‐a‐chip” methods that vastly miniaturize cellulmical experiments could transform the speed, cost, and success of multiple workstreams in biologics development. Several microscale bioprocess technologies have been established that incrementally address these needs, yet each is inflexibly designed for a very specific process thus limiting an integrated holistic application. A more fully integrated nanoscale approach that incorporates manipulation, culture, analytics, and traceable digital record keeping of thousands of single cells in a relevant nanoenvironment would be a transformative technology capable of keeping pace with today's rapid and complex drug discovery demands. The recent advent of optical manipulation of cells using light‐induced electrokinetics with micro‐ and nanoscale cell culture is poised to revolutionize both fundamental and applied biological research. In this review, we summarize the current state of the art for optical manipulation techniques and discuss emerging biological applications of this technology. In particular, we focus on promising prospects for drug discovery workflows, including antibody discovery, bioassay development, antibody engineering, and cell line development, which are enabled by the automation and industrialization of an integrated optoelectronic single‐cell manipulation and culture platform. Continued development of such platforms will be well positioned to overcome many of the challenges currently associated with fragmented, low‐throughput bioprocess workflows in biopharma and life science research.

Next-generation flexible formats of VNAR domains expand the drug platform's utility and developability.

Therapeutic mAbs have delivered several blockbuster drugs in oncology and autoimmune inflammatory disease. Revenue for mAbs continues to rise, even in the face of competition from a growing portfolio of biosimilars. Despite this success, there are still limitations associated with the use of mAbs as therapeutic molecules. With a molecular mass of 150 kDa, a two-chain structure and complex glycosylation these challenges include a high cost of goods, limited delivery options, and poor solid tumour penetration. There remains an urgency to create alternatives to antibody scaffolds in a bid to circumvent these limitations, while maintaining or improving the therapeutic success of conventional mAb formats. Smaller, less complex binders, with increased domain valency, multi-specific/paratopic targeting, tuneable serum half-life and low inherent immunogenicity are a few of the characteristics being explored by the next generation of biologic molecules. One novel 'antibody-like' binder that has naturally evolved over 450 million years is the variable new antigen receptor (VNAR) identified as a key component of the adaptive immune system of sharks. At only 11 kDa, these single-domain structures are the smallest IgG-like proteins in the animal kingdom and provide an excellent platform for molecular engineering and biologics drug discovery. VNAR attributes include high affinity for target, ease of expression, stability, solubility, multi-specificity, and increased potential for solid tissue penetration. This review article documents the recent drug developmental milestones achieved for therapeutic VNARs and highlights the first reported evidence of the efficacy of these domains in clinically relevant models of disease.

Considerations for implementing an informatics system to support biologics drug discovery

A comprehensive, well-functioning and scientifically aware informatics environment is of the utmost importance in supporting effective drug discovery programs. However, implementing such a system can, without a carefully crafted and enacted strategy, be a disruptive and time-consuming process, fraught with risks of cost overruns and the potential to end up with a system that ultimately does not meet the ever-evolving needs of the organization. In this review, using our experience from the software provider perspective, we discuss how a drug discovery organization should approach the task of selecting an informatics system to support its research discovery programs. We focus on biologics drug discovery because: (i) in general, biologics informatics is less mature than small-molecule discovery; (ii) there is a great deal of activity in biologics drug discovery, from new biologics-only companies to established small-molecule companies extending into biologics programs; and (iii) by their nature, biologics can be more challenging than small molecules to support, owing to the size, complexity and diversity of biologics entities. These factors make decisions about which system(s) to implement even more challenging.

Abstract PR06: Drugging the human microbiome for combination with tumor immunotherapy

Abstract The human gut microbiome is a diverse, dynamic, and complex ecosystem that modulates host processes including metabolism, inflammation, and cellular and humoral immune responses. Recent studies have suggested that the microbiome may also influence the development of certain cancers such as colorectal cancer, and equally importantly, tumor response to systemic therapy, especially immunotherapy. Multiple groups are exploring the therapeutic utility of the microbiome to enhance clinical response through the use of defined oral therapeutics comprising living commensal bacteria, which would represent a new therapeutic modality. Exploiting the microbiome for therapeutic benefit is not without its challenges due to the heterogeneity of the gut microbiota across healthy donors and patients. In addition, many aspects of conventional small molecule and biologics drug discovery and development do not apply to this novel class of living drugs. We present an approach that leverages the concept of “reverse translation,” using genomic and immunologic characterization of patient samples from interventional studies to define and better understand the organisms and mechanisms that contribute to response or non-response to immunotherapy. We are investigating the relationship between the composition of the gut microbiome prior to therapy and the antitumor response in patients receiving checkpoint inhibitors (CPI), as well as how CPI treatment modulates the microbiome in both responders and nonresponders. Fecal and blood samples are collected before and during therapy from cancer patients who receive approved CPI; tumor types include renal, bladder, and NSCLC. Whole metagenomic shotgun sequencing of patient microbiomes is used to identify higher order (e.g., order- and family-level) “microbial signatures” that associate with response to CPI treatment. We then utilize proprietary algorithms that enable species- and strain-level resolution of microbial signatures. In addition, global and targeted metabolomics are used to identify functional pathways associated with outcome, and these pathways can be linked to species and strains identified by genomic analysis. Our discovery strategy iterates computational analyses and machine learning approaches with empirical in vitro and ex vivo screening of strains and consortia to inform selection and drive drug design. Data from such a comprehensive approach is invaluable for designing compositions of bacteria that form “functional ecological networks” that can impact response to CPI therapy. Finally, our microbial library of &amp;gt;14,000 isolates from healthy human subjects captures the phylogenetic diversity and functional breadth of the gastrointestinal microbiome, and provides a robust platform to build unique compositions. Such compositions, when tested in syngeneic tumor models in germ-free mice, can provide a preliminary readout of the contributions of members of the consortia and enable candidate identification. We present examples of reverse translation in patients with recurrent Clostridium difficile infection and ulcerative colitis, a form of inflammatory bowel disease, that have led to the translation of three drugs that are currently in clinical trials. This roadmap provides insight into how similar drugs can be discovered and developed in the setting of immunotherapy to augment the efficacy of CPIs by altering the cancer-immune set point. This abstract is also being presented as Poster A06. Citation Format: David N. Cook, Jonathan Peled, Marcel van den Brink, Lata Jayaraman. Drugging the human microbiome for combination with tumor immunotherapy [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr PR06.

Metabolomics: Bridging Chemistry and Biology in Drug Discovery and Development

Purpose of Review Metabolism, as a ubiquitous biological process, plays a decisive role in the wellbeing of cells, organs, and whole body. Since the endpoint of pharmacological intervention is to either recover or sustain the wellbeing of targeted biological systems, examining metabolic events reveals useful information on diseases and drug treatment. Based on its omics nature and capacity to examine both drug and endogenous metabolism, metabolomics is an ideal systems biology tool to examine chemical and metabolic events in drug discovery and development.