A head-to-head comparison of the inhibitory activities of 15 peptidomimetic SARS-CoV-2 3CLpro inhibitors.

The COVID-19 pandemic caused by SARS-CoV-2 has created an unprecedented global health emergency. As of July 2021, only three antiviral therapies have been approved by the FDA for treating infected patients, highlighting the urgent need for more antiviral drugs. The SARS-CoV-2 3CL protease (3CLpro) is deemed an attractive drug target due to its essential role in viral polyprotein processing and pathogenesis. Indeed, a number of peptidomimetic 3CLpro inhibitors armed with electrophilic warheads have been reported by various research groups that can potentially be developed for treating COVID-19. However, it is currently impossible to compare their relative potencies due to the different assays employed. To solve this, we conducted a head-to-head comparison of fifteen reported peptidomimetic inhibitors in a standard FRET-based SARS-CoV-2 3CLpro inhibition assay to compare and identify potent inhibitors for development. Inhibitor design and the suitability of various warheads are also discussed.

Targeting cancer addiction for SALL4 by shifting its transcriptome with a pharmacologic peptide.

Sal-like 4 (SALL4) is a nuclear factor central to the maintenance of stem cell pluripotency and is a key component in hepatocellular carcinoma, a malignancy with no effective treatment. In cancer cells, SALL4 associates with nucleosome remodeling deacetylase (NuRD) to silence tumor-suppressor genes, such as PTEN. Here, we determined the crystal structure of an amino-terminal peptide of SALL4(1-12) complexed to RBBp4, the chaperone subunit of NuRD, at 2.7 Å, and subsequent design of a potent therapeutic SALL4 peptide (FFW) capable of antagonizing the SALL4-NURD interaction using systematic truncation and amino acid substitution studies. FFW peptide disruption of the SALL4-NuRD complex resulted in unidirectional up-regulation of transcripts, turning SALL4 from a dual transcription repressor-activator mode to singular transcription activator mode. We demonstrate that FFW has a target affinity of 23 nM, and displays significant antitumor effects, inhibiting tumor growth by 85% in xenograft mouse models. Using transcriptome and survival analysis, we discovered that the peptide inhibits the transcription-repressor function of SALL4 and causes massive up-regulation of transcripts that are beneficial to patient survival. This study supports the SALL4-NuRD complex as a drug target and FFW as a viable drug candidate, showcasing an effective strategy to accurately target oncogenes previously considered undruggable.

Miniature bovine pancreatic trypsin inhibitors (m-BPTIs) of the West Nile virus NS2B-NS3 protease.

The mosquito-borne West Nile virus (WNV) causes a wide range of symptoms ranging from fever to the often fatal viral encephalitis. To date, no vaccine or drug therapy is available. The trypsin-like WNV NS2B-NS3 protease is deemed a plausible drug target and was shown to be inhibited by bovine pancreatic trypsin inhibitor (BPTI), a 58-residue protein isolated from bovine lung. Herein, we report a protein truncation study that resulted in a novel 14-residue cyclic peptide with equipotent inhibitory activity to native BPTI. We believe our truncation strategy can be further applied in the development of peptide-based inhibitors targeting trypsin-like proteases.

Peptidomimetic ethyl propenoate covalent inhibitors of the enterovirus 71 3C protease: a P2-P4 study.

Enterovirus 71 (EV71) is a highly infectious pathogen primarily responsible for Hand, Foot, and Mouth Disease, particularly among children. Currently, no approved antiviral drug has been developed against this disease. The EV71 3C protease is deemed an attractive drug target due to its crucial role in viral polyprotein processing. Rupintrivir, a peptide-based inhibitor originally developed to target the human rhinovirus 3C protease, was found to inhibit the EV71 3C protease. In this communication, we report the inhibitory activities of 30 Rupintrivir analogs against the EV71 3C protease. The most potent inhibitor, containing a P2 ring-constrained phenylalanine analog (compound 9), was found to be two-fold more potent than Rupintrivir (IC50 value 3.4 ± 0.4 versus 7.3 ± 0.8 µM). Our findings suggest that employing geometrically constrained residues in peptide-based protease inhibitors can potentially enhance their inhibitory activities.

Cytotoxic activity and cell specificity of a novel LHRH peptide drug conjugate, D-Cys6-LHRH vedotin, against ovarian cancer cell lines.

Ovarian cancer is the most deadly female gynaecological malignancy in developed countries and new treatments are urgently needed. The luteinising hormone releasing hormone (LHRH) peptide drug conjugate Zoptarelin doxorubicin is one such potential new drug modality that entered clinical trials for treating LHRH receptor-positive gynaecological cancers. However, development stopped after disappointing Phase 3 results in 2017. We believe the lack of efficacy was due to linker instability and payload potency. In this work, we replaced its linker-toxin with vedotin (MC-VC-PABC-MMAE), yielding the novel peptide drug conjugate D-Cys6-LHRH vedotin. A GI50 and cell specificity comparison against cancerous and non-cancerous ovarian cell lines showed significantly superior bioactivity and selectivity over Zoptarelin doxorubicin (GI50 4 vs. 453 nM) and other chemotherapeutic drugs used for treating ovarian cancers. Our results suggest D-Cys6-LHRH vedotin can potentially be used as a treatment for ovarian cancer.

Novel PSMA-Targeting Radionuclide Peptidomimetics for Treating Prostate Cancer.

Prostate cancer is the third-most commonly diagnosed cancer and is one of the leading causes of cancer-related deaths in men worldwide. Although an armamentarium of approved drugs exists, treatment options become severely limited when resistance develops against last-line taxane chemotherapeutics. In March 2022, the FDA approved a first-in-class targeted radionuclide therapy, lutetium Lu 177 vipivotide tetraxetan (Pluvicto), for treating metastatic castration-resistant prostate cancer. The drug constitutes a prostate-specific membrane antigen-targeting peptidomimetic moiety conjugated to a radionuclide chelator via a linker. This Patent Highlight reveals the structure-activity relationship of key compounds against prostate cancer cells.

Novel Nitrile Peptidomimetics for Treating COVID-19.

COVID-19 is a highly infectious disease caused by the viral pathogen SARS-CoV-2, causing an estimated 5.4 million fatalities globally in 2 years since its emergence in December 2019. On December 22, 2021, the U.S. FDA granted Emergency Use Authorization for the oral viral main protease inhibitor, Nirmatrelvir, to treat patients with mild-to-moderate COVID-19. This patent review reveals the structure-activity relationship of key inhibitors described in the patent WO 2021/250648 A1.

A Patent Review on FDA-Approved Antibody-Drug Conjugates, Their Linkers and Drug Payloads.

Antibody-drug conjugates (ADCs) have emerged as a promising class of biologics since the first approval of Gemtuzumab ozogamicin in 2000. Compared to small molecule drugs, ADCs are structurally much more complex as they comprise of an antibody conjugated to cytotoxic payloads by specially-designed linkers. Correspondingly, the ADC patent landscape is also much more complex. This review collates and discusses the patents protecting ADCs approved by the FDA up to 31 December 2021, with particular emphasis on their linker and cytotoxin payload technologies.

Novel Halomethylketone Azadipeptides for Treating COVID-19.

COVID-19 is a highly infectious disease caused by the SARS-CoV-2 coronavirus. It rapidly escalated into a global pandemic, causing more than 6 million fatalities by March 2022, a little over 2 years since its emergence in December 2019. The first peptidomimetic coronavirus main protease inhibitor, nirmatrelvir, was granted Emergency Use Authorization by the U.S. FDA on Dec 22, 2021. Less than a month after its patent application, Hoffmann La-Roche scientists filed a patent application describing azadipeptide peptidomimetic inhibitors (WO 2022/043374 A1). This patent highlight reveals the structure-activity relationship of key azadipeptide inhibitors described in the patent.

A Patent Review on SARS Coronavirus Main Protease (3CLpro ) Inhibitors.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is an unprecedented global health emergency causing more than 4.2 million fatalities as of 30 July 2021. Only three antiviral therapies have been approved or granted emergency use authorization by the FDA. The SARS-CoV-2 3CL protease (3CLpro ) is deemed an attractive drug target as it plays an essential role in viral polyprotein processing and pathogenesis, although no inhibitors have been approved. This patent review discusses SARS coronavirus 3CLpro inhibitors that have been filed up to 30 July 2021, giving an overview on the types of inhibitors that have generated commercial interest, especially amongst drug companies. Insights into the common structural motifs required for active site binding is also discussed.

Oral Nonpeptidic, Noncovalent Triazine Coronavirus Main Protease Inhibitors for Treating COVID-19.

The current COVID-19 global pandemic caused by SARS-CoV-2 has claimed more than 6 million lives since its emergence in December 2019. The first oral coronavirus main protease inhibitor, nirmatrelvir, was granted Emergency Use Authorization by the U.S. FDA in December 2021, with a twice-daily dosing regimen in combination with ritonavir. In March 2022, Shionogi & Co. announced their single-agent, once-daily oral SARS-CoV-2 main protease inhibitor, ensitrelvir, was granted approval for global phase 3 clinical trials. Unlike nirmatrelvir, ensitrelvir is a nonpeptidic, noncovalent, small molecule. This Patent Highlight describes key structures and their inhibitory activities in Shionogi & Co.'s and Hokkaido University's patent WO 2022/138987 A1.

Novel Coronavirus Main Protease Di- and Tripeptide Inhibitors for Treating COVID-19.

COVID-19 is a highly infectious disease caused by SARS-CoV-2. First reported in December 2019, it rapidly escalated into a global pandemic, resulting in over 6.3 million fatalities by July 4, 2022. The first oral coronavirus main protease inhibitor, nirmatrelvir, was granted Emergency Use Authorization by the U.S. FDA in December 2021. It is a tripeptide incorporated with a C-terminal nitrile designed to bind and form a covalent attachment to the SARS-CoV-2 main protease. Shortly after nirmatrelvir's approval, Enanta Pharmaceuticals' peptidomimetic SARS-CoV-2 main protease inhibitor entered clinical trials in February 2022. This patent highlight reports key structures of di- and tripeptide inhibitors described in Enanta Pharmaceuticals' patent WO 2022/020242 A1.

Preliminary investigations into developing all-D Omiganan for treating Mupirocin-resistant MRSA skin infections.

Staphylococcus aureus is the primary pathogen responsible for the majority of human skin infections, and meticillin-resistant S. aureus (MRSA) currently presents a major clinical concern. The overuse of Mupirocin, the first-line topical antibacterial drug over 30 years, has led to the emergence of Mupirocin-resistant MRSA, creating a clinical concern. The antimicrobial peptide Omiganan was touted to be a promising antibacterial drug candidate due to its rapid membrane-disrupting bactericidal mode of action, entering clinical trials in 2005 as a topical gel to prevent catheter site infections. However, drug development ceased in 2009 due to a lack of efficacy. We postulate this to be due to proteolytic degradation caused by endogenous human skin proteases. Herein, we tested our hypothesis using Omiganan and its all-D enantiomer in a human skin protease stability assay, followed by anti-MRSA activity assay against of a panel of clinical MRSA isolates, a bactericidal/static determination and a time-kill assay to gauge all-D Omiganan's potential for further topical antibacterial drug development.

Application of Fragment-Based Drug Discovery against DNA Gyrase†B.

Bacterial resistance to antibiotics remains a serious threat to global health. The gyrase B enzyme is a well-validated target for developing antibacterial drugs. Despite being an attractive target for antibiotic development, there are currently no gyrase B inhibitory drugs on the market. A fragment screen using 1,800 compounds identified 14 fragments that bind to Escherichia coli (E. coli) gyrase B. The detailed characterization of binding is described for all 14 fragments. With the aid of X-ray crystallography, modifications on a low-affinity fragment (KD =253 µM, IC50 =634 µM) has led to the development of a new class of potent phenyl aminopyrazole inhibitors against E. coli gyrase B (IC50 =160 nM). The study presented here combines the use of a set of biophysical techniques including differential scanning fluorimetry, nuclear magnetic resonance, isothermal titration calorimetry, and X-ray crystallography to methodically identify, quantify, and optimize fragments into new chemical leads.

A P2 and P3 substrate specificity comparison between the Murray Valley encephalitis and West Nile virus NS2B/NS3 protease using C-terminal agmatine dipeptides.

The Murray Valley encephalitis virus (MVEV) and the West Nile virus (WNV) are mosquito-borne single-stranded RNA Flaviviruses responsible for many cases of viral encephalitis and deaths worldwide. The former is endemic in north Australia and Papua New Guinea while the latter has spread to different parts of the world and was responsible for a recent North American outbreak in 2012, resulting in 243 fatalities. There is currently no approved vaccines or drugs against MVEV and WNV viral infections. A plausible drug target is the viral non-structural NS2B/NS3 protease due to its role in viral replication. This trypsin-like serine protease recognizes and cleaves viral polyproteins at the C-terminal end of an arginine residue, opening an avenue for the development of peptide-based antivirals. This communication compares the P2 and P3 residue preferences of the MVEV and WNV NS2B/NS3 proteases using a series of C-terminal agmatine dipeptides. Our results revealed that both viral enzymes were highly specific toward lysines at the P2 and P3 positions, suggesting that a peptidomimetic viral protease inhibitor developed against one virus should also be active against the other.

Membrane binding and perturbation studies of the antimicrobial peptides caerin, citropin, and maculatin.

Citropin 1.1, maculatin 1.1, and caerin 1.1 are short antibacterial cationic peptides from the skin glands of the Australian tree frog Litoria species. Several analogues have been synthesized to give a better insight into the relationship between the structure of the peptides and their antibacterial and haemolytic activity. Binding studies using a surface plasmon resonance (SPR) biosensor together with a vesicle-capture sensor chip have been used to investigate selectivity of the peptides and their analogues for 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) vesicles, as well as for vesicles made from lipid extracts from Escherichia coli and bovine brain. Data obtained for membrane selectivity using natural lipid extracts show better correlation with minimum inhibitory concentration (MIC) values against Gram-positive bacteria and haemolytic activity than that obtained using synthetic DMPG and DMPC. Electron microscopy and membrane leakage studies using Gram-positive bacteria gave further insight into the membrane disruption properties of the peptides. For maculatin 1.1, it was found that the central proline residue, which is responsible for a bend in the alpha-helical structure, is essential not only for the antibacterial activity but also for binding, and perturbation of membranes. The caerin analogues showed only small variations in their MIC values and membrane binding. In contrast, for citropin 1.1, the analogue replacing the aspartate with a lysine showed the lowest MIC against Gram-positive bacteria and best membrane binding to E. coli lipid extracts, coinciding with an increased hydrophobic moment of the peptide. These data give further insight into these antimicrobial natural products, toward the development and evaluation of these and other analogues as potential antibiotics.