Tag Archives: immunotherapy

The Needle Issue #14

9 Sep
Juan-Carlos-Lopez
Juan Carlos Lopez		 Andy-Marshall
Andy Marshall

It is now nearly a decade since Dublin-based startup ​Inflazome burst onto the scene with the description of MCC950, the first nanomolar selective inhibitor of the inflammasome. Inflammasome-mediated low-grade inflammation has been associated with cancers, numerous chronic complex diseases—including inflammatory bowel disease, arthritis, metabolic dysfunction-associated steatohepatitis (MASH), atherosclerosis, Alzheimer’s, Parkinson’s and ALS—as well as rare autoinflammatory diseases, such as cryopyrin-associated periodic syndromes (CAPS). There is a wealth of compelling human genetic evidence from Muckle-Wells syndrome and other autosomal dominant familial genetic diseases showing gain-of-function mutations in NLRP3 are causative of autoinflammatory disease.

Given the ‘pipeline in a product’ potential of drugs targeting this pathway, big pharma has shown considerable interest, with Genentech/Roche snapping up Jecure Therapeutics for an undisclosed amount, and both Novartis and Roche splashing out hundreds of millions of dollars for pioneer companies IFM Tre and Inflazome, respectively. In 2022, Novo Nordisk licensed Ventus Therapeutics’ peripherally restricted NLRP3 inhibitor in a deal worth up to $703 million, lending weight to pharmacological inhibition of NLRP3 as a complement to glucagon-like peptide-1 agonists (GLP-1s) in cardiometabolic disease. And with several programs now entering the clinic, investment activity in the area has continued, with Enveda’s announcement last week of a $150 million series D round to fund a phase 1 trial for ENV-6946, an orally delivered gut-restricted small molecule targeting the NLRP3/tumor necrosis factor-like cytokine 1A (TL1A) pathway in inflammatory bowel disease.

Today, Haystack counts at least 17 independent companies pursuing inflammasome therapeutics (AC Immune, Azome Therapeutics, BioAge Labs, Cardiol Therapeutics, EpicentRx, Enveda, Halia Therapeutics, InflammX Therapeutics, Insilico Medicine, Neumora Therapeutics, NodThera, Olatec Therapeutics, Shaperon, Ventus Therapeutics, Ventyx Biosciences, ZyVersa Therapeutics and Zydus LifeSciences) and 8 programs now in clinical testing specifically targeting the key inflammasome component NLRP3.

While drugmakers have traditionally targeted downstream extracellular mediators of the inflammasome pathway (canakinumab or rilonacept against IL-1β or anakinra to block IL-1 receptor), NLRP3 represents a key upstream intracellular signaling hub, activated by innate immune pattern-recognition receptor (Toll like receptors 2/4) signaling via MyD88 and NFkappaB. Once activated, NLRP3 monomers unfold and associate into a massive 1.2 MDa oligomeric supracomplex with three other proteins: ASC, NEK7 and caspase 1. The mature complex then cleaves and activates proinflammatory cytokines interleukin (IL)-1β and IL-18 and primes gasdermin D to instigate cell pore formation and cell death via pyroptosis.

Discovering effective drugs against NLRP3 has proven challenging. The first NMR structure was obtained in 2016, but the structural basis for how NLRP3 ring-like oligomers associate with intracellular membranes and how its pyrin domains associate with ASC to orchestrate speck formation and caspase activation have only recently been elucidated. Thus far, the majority of small-molecule inhibitors (e.g., Inflazyme’s archetypal MCC950 and inzolemid; Zydus’s (ZYIL1), Olatec’s OLT117 and Jecure Therapeutics’ GDC-2394) form hydrogen bonds via a sulfonylurea group to NLRP3’s NACHT domain nucleotide-binding motifs, thereby obstructing ATP hydrolysis. Other companies are taking a different tack: thus, Halia Therapeutic’s small-molecule inhibitor orniflast and Monte Rosa Therapeutics’ MRT-8102 molecular glue target NEK7 rather than NLRP3.

But it has been less than straightforward to identify compounds with sufficient potency to target this pivotal innate immune signaling pathway without debilitating off-target effects. Indeed, several of the first wave of compounds entering the clinic have been dogged by serious toxicities, including liver problems (MCC950 and GDC-2394) and hypoglycemia (glyburide). Now, a team led by Rebecca Coll (Queen’s University Belfast) and Kevin Wilhelmsen (of BioAge Labs) reports in The Journal of Experimental Medicine the discovery and characterization of BAL-0028, a novel and selective small-molecule inhibitor of the human NLRP3 inflammasome.

Unlike previously studied inhibitors, BAL-0028 acts through a unique mechanism of action; it binds NLRP3’s NACHT domain at a site distinct from other inhibitors that act by directly interfering with ATPase activity. BAL-0028 has nanomolar potency against human and primate NLRP3 but, remarkably, has weak activity against the mouse target, highlighting species-specific differences.

As BAL-0028 showed very high plasma protein binding in mice, limiting its use in vivo, the team developed a derivative, BAL-0598, with improved pharmacokinetic properties. In a humanized NLRP3 mouse peritonitis model, BAL-0598 effectively reduced IL-1β and IL-6 production, confirming its anti-inflammatory activity in vivo. Importantly, both BAL-0028 and BAL-0598 inhibited hyperactive NLRP3 mutants associated with autoinflammatory diseases, in some cases more effectively than Vertex’s VX-765, a caspase 1 inhibitor, and compounds like MCC950, one of the best characterized NLRP3 inhibitors available.

The novel mechanism of action of BAL-0028 and BAL-0598 would suggest their off-target effects may be different from those associated with other NLRP3 inhibitors blocking ATP hydrolysis. The concern that such compounds might also bind other members of the NOD/NLR family (e.g., NLRP1, NLRP4 or AIM2 inflammasomes) is mitigated by most published studies indicating that NLRP3’s unique fold around the ATP binding site makes small-molecule binders selective for this family member alone. The most likely explanation from trials published to date is that the observed toxicities are associated with small molecule chemotype rather than any NLRP3 class-specific problem. In any case, the findings from this study support further investigation of these compounds as candidates for treating inflammatory and age-related diseases where NLRP3 plays a role. The race to develop a safe and effective NLRP3 inhibitor is on, with big pharma billion-dollar bets and startups jostling to create best-in-class assets across cancer, cardiovascular, neurodegenerative and metabolic disease.

​

Tags: , , , , , , , , , , , , , , , , , , , ,

The Needle Issue #13

3 Sep
Juan-Carlos-Lopez
Juan Carlos Lopez		 Andy-Marshall
Andy Marshall

While most parts of biotech early-stage financing have been in the doldrums in the past two or three years, so-called tech-bio startups have been thriving. Since the posterchild $1.0 billion mega series A round last April of Xaira Therapeutics, which was founded by scientists out of Nobel prize winner David Baker’s group at the University of Washington, several startups seeking to develop machine learning models for designing miniproteins or peptide binders of challenging or ‘undruggable’ targets have emerged, including Enlaza Therapeutics, Vilya, and UbiquiTx. All of these have been developing their own proprietary models based on Alphafold 3, Boltz-1 or Chai-1 for structure prediction and tools based off RFdiffusion, Bindcraft and ProteinMPNN for peptide design. Predicting CDR loops for de novo antibody design is a considerably more challenging task than for simple peptides, but Nabla Bio, founded last year by scientists out of George Church’s lab at Harvard, claims it is doing just that for GPCRs and ion channels. Earlier this month, Chai Discovery also launched with a $100 million series A from Menlo Ventures to optimize multimodal generative models such as Chai-2, which, according to the company, already “achieves a 16% hit rate in de novo antibody design.”

Designing peptides that can selectively bind to a protein target and show therapeutic activity remains a challenge, however, as it often depends on the availability of high-quality structural information about the target molecule, which is seldom available for many disease-relevant proteins that are unstructured or conformationally disordered. Similarly modeling protein-protein interactions like antibody-antigen interactions that are extremely dynamic and floppy also poses problems. All of which raises the question as to whether binders could be predicted simply using amino acid sequence information instead of structural data.

Now, a team led by Pranam Chatterjee from Duke University has addressed this question. In a recent paper in Nature Biotechnology, Chatterjee and his collaborators report the creation of PepMLM, a peptide binder design algorithm based on masked language modeling. A key feature of the algorithm is that it depends exclusively on protein sequence, not structure. Built upon the ESM-2 (Evolutionary Scale Modeling 2) protein language model, PepMLM masks and reconstructs entire peptide regions appended to target protein sequences. This design compels the model to generate context-specific binders. To train PepMLM, the team used high-quality curated datasets from PepNN and Propedia comprising ~10k putative peptide-protein sequence pairs. PepMLM output was consistently found to outperform RFDiffusion on held-out/structured targets, with a higher hit rate (38% to 29%) and low perplexities that closely matched real binders, with generated sequences showing target specificity, even in stringent permutation tests.

The model generated binders predicted to have higher binding scores than native and structure-based binders designed through other methods. Indeed, in vitro validation experiments confirmed the high affinity and specificity of PepMLM-generated binders.

Chatterjee and his colleagues went on to turn their binders into degraders by fusing them to E3 ubiquitin ligase domains, such as CHIP/STUB1. When tested in vitro, over 60% of these degraders knocked down their target proteins. PepMLM peptides achieved nanomolar binding affinity on the drug targets neural cell adhesion molecule 1 (NCAM1), a key marker of acute myeloid leukemia, and anti-Müllerian hormone type 2 receptor (AMHR2), a critical regulator of polycystic ovarian syndrome (where RFDiffusion-predicted peptides failed to bind). The authors also demonstrated that PepMLM-predicted peptides fused to E3 ubiquitin ligases not only degraded MSH3 but completely eliminated mutant huntingtin protein exon 1 containing 43 CAG repeats in Huntington disease patient-derived fibroblast cells. Similar results were obtained for a PepMLM-predicted peptide binder of MESH1, a protein controlling ferroptosis, in collaboration with Ashley Chi Jen-Tsan’s group at Duke University (RFDiffusion again gave no hits). And with Madelaine Dumas and Hector Aguilar-Carreno’s group, in collaboration with Matt Delisa’s group at Cornell University, PepMLM-derived peptides bound and reduced levels of viral phosphoproteins from Nipah, Hendra, and human metapneumovirus (HMPV); indeed, in live HMPV infection models, the PepMLM peptide mediated high levels of P protein clearance.

The ability of PepMLM to design binders purely on the basis of target-protein sequence is an important advance towards designing therapeutic peptides against hitherto inaccessible targets that lack structural data. Future work should explore how to incorporate chemical modifications such as cyclization or stapling to enhance stability of the binders, as well as the evaluation of the strongest candidates in vivo. Another challenge will be to ameliorate the immunogenicity of these foreign de novo proteins. The use of protein engineering approaches, such as incorporation of mirror amino acids that can cloak foreign peptides from the immune system, may offer solutions. But it is likely that candidates discovered using sequence or structure prediction tools will still require lengthy development programs to be turned into safe and effective drugs, despite the hype.

Tags: , , , , , , , , , , , , , , , , , , ,

The Needle Issue #12

12 Aug
Juan-Carlos-Lopez
Juan Carlos Lopez		 Andy-Marshall
Andy Marshall

The Summer BIO report “The State of Emerging Biotech Companies: Investment, Deal, and Pipeline Trends” highlights how much China-based programs have contributed to the drug pipeline over the past 10 years.

A couple of weeks ago, Bloomberg also summarized deal data showing how the share of global licensing by Chinese biotech companies has jumped over the past two years.

Judging by a report listing 16 ‘high-value’ currently unlicensed assets from China being hawked by longtime Phalanx Investment Partners analyst David Maris, there is more licensing to come.

In this context, we read with interest a recent Science Immunology paper describing a monoclonal antibody (mAb) program targeting a novel phagocytic checkpoint under development at yet another Chinese biotech: MedimScience, founded in Hangzhou City in 2021. MedimScience is one of a growing cadre of companies, including LTZ Therapeutics, Dren Bio, Chengdu Kanghong, Antengene and ImmuneOnco, looking to develop novel myeloid cell engagers/phagocytic checkpoint inhibitors.

Phagocytic checkpoint inhibitors are drugs that circumvent the molecular cloaks that tumors throw around themselves to avoid uptake and destruction by myeloid cells, such as macrophages, monocytes, and neutrophils. The strategy first came to the fore through pioneering work on the ‘don’t eat me’ signal CD47, work carried out by Ravi Majeti and Irv Weissman at Stanford. Results from their preclinical studies spurred the launch of startup Forty Seven (subsequently acquired in 2020 by Gilead) and the first-in-class anti-CD47 IgG4 magrolimabprogram.Phase 1b trial results of magrolimab combined with azacitidine in acute myeloid leukemia (AML) patients were so impressive that, by 2022, more than 20 different companies had anti-CD47 programs in clinical development. This blew up spectacularly when early trials failed to be reproduced in larger efficacy trials of combinations — failure that was largely attributed to intolerability/anemia issues related to the target, slow action/early disease progression, and a failure to account for patient heterogeneity with regard to P53 mutation status. But the strategy is compelling and the hunt for new phagocytic checkpoints has continued with new antibody formats seeking to avoid these pitfalls.

Now, Cheng Zhong and his colleagues at MedimScience report the identification of a new evasion actor — PSGL-1 — that suppresses macrophage-mediated phagocytosis in a variety of hematological malignancies. PSGL-1, which was previously known largely for its role in cell adhesion, is highly expressed in various hematologic cancers, including AML, T-acute lymphoblastic leukemia (T-ALL) and multiple myeloma (MM).

Moreover, high PSGL-1 expression has been found to correlate with poor patient survival in AML, T-ALL and MM.

Using several mouse models, the researchers found that tumors lacking PSGL-1 show slower progression, increased macrophage infiltration, and higher rates of phagocytosis by macrophages, effects that were independent of T cells or dendritic cells.

Mechanistically, the team found that PSGL-1 disrupts the interaction between the cell-adhesion molecule ICAM-1 on tumor cells and the integrin LFA-1 (CD11a/CD18) on macrophages. And when they tested Novartis’ lifitegrast, an inhibitor of ICAM-1/LFA-1 binding, they found this largely abrogates the phagocytosis of PSGL-1 knockout tumor cells, confirming PSGL1’s role in impairing prophagocytic signaling and cytoskeletal reorganization required for effective tumor-cell engulfment.

The authors went on to develop a humanized mAb against PSGL-1 and show its ability to induce phagocytosis of human tumor cells in vitro and to reduce tumor burden in mouse models of AML, T-ALL, and MM. The antibody showed a good safety profile in non-human primates with no significant toxicity at high doses. Additionally, PSGL-1 blockade synergized with chemotherapy (doxorubicin) and antibody-based therapies (anti-CD47 and anti-CD38), further underscoring the translational potential of this strategy, particularly in treatment-resistant settings.

Tags: , , , , , , , , , , , , , , , , ,

Newer Entries →