ChemPartner Blog

By: Dr. Jie Jack Li, Vice President of Discovery Chemistry at ChemPartner On June 16th, 2020, a team at Oxford University announced that their RECOVERY trials had revealed that a daily treatment of 6 mg of dexamethasone (Decadron, 1) lowered the fatality rate of ventilated COVID-19 patients by up to one third! This was a randomized, double-blinded clinical trial, the gold standard, thus lending much credibility to the results. It seems to work even better than Gilead’s remdesivir (Veklury, 2) for this group of seriously ill patients. Moreover, dexamethasone (1) is cheap, widely available, and it has been used for more sixty years in the clinics. Let us take a journey to look at how dexamethasone (1) was discovered, how it has become almost a panacea for all ills in medical practice, how it works to benefit COVID-19 patients, and how it is made. A group of chemists at Merck discovered dexamethasone (1), a steroid hormone, in 1958 as an anti-inflammatory steroid.1 Merck marketed dexamethasone (1) with a brand name Decadron in 1959. As a testimony to how competitive the field was during the golden age of steroid hormone drugs, Schering Corporation simultaneously synthesized the same compound as well. Considering the two companies merged in 2009, it matters not today with regard to priority. Inflammation and immunity, like all other normal reactions of the body, are meant to preserve or restore health. Classic inflammatory diseases include rheumatoid arthritis and Crohn’s disease (an inflammatory bowel disease). Rheumatoid arthritis is a chronic inflammatory disease characterized by pain, swelling, and subsequent destruction of joints. Philip S. Hench and Edward C. Kendall at the Mayo Clinic discovered cortisone (3) and isolated it from bovine adrenal cortex (a small organ attached to the top of the kidney, cortex means out-layer). In 1948, Hench gave cortisone...
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By: Dr. Jie Jack Li, Vice President of Discovery Chemistry at ChemPartner Gileadʹs antiviral drug remdesivir (Veklury, 1) was approved by the FDA on May 1st for emergency use against coronavirus disease-2019 (COVID-19) after just a one-day review. Now the onerous task falls upon Gilead to make enough of the drug to supply doctors and patients around the world. But one wonders: how is remdesivir made? Remdesivir (1) is a ProTide, a phosphoramidate prodrug of nucleoside GS-44154 (2), which consists of two parts: the ribose core and the unnatural base. Two generations of synthesis of remdesivir (1) have been reported by Gilead. a. The First Generation Synthesis Gilead published two papers in 2012, one on medicinal chemistry,1 and the other on a practical synthesis of GS-44154 (2) and its analogs.2 As shown in the scheme below, pyrrolotriazine-bromide 4 was prepared according to a Bayer patent (vide infra).3 The bis-silylchloride 5 was a “transient” protective group. It capped the amine group on pyrrolotriazine-bromide 4 first, which would allow the subsequent halogen-metal exchange between the bromide 4 and n-BuLi. To the lithiated intermediate was added commercially available benzyl protected ribonolactone 3, giving rise to adduct lactol 6 as a mixture of diastereomers at the 1ʹ-position. The bis-silyl protective group was removed during acidic workup. Subsequently, in the presence of a Lewis acid (BF3•OEt2), lactol 6 was treated with TMS-CN to provide nitrile 7 as a mixture of 85:15 ratio favoring the b-anomer. BCl3-promoted debenzylation provided the desired nucleoside as GS-44154 (2) after chromatographic separation of the two diastereomers.1,2 As eluded earlier, pyrrolotriazine 4 was prepared according to a Bayer patent that covered insulin-like growth factor 1 receptor (IGF-1R) kinase inhibitors for treating cancer.3 To that end, condensation between 2,5-dimethoxytetrahydrofuran (8) and tert-butylcarbazate (9) in the presence of 2 N HCl gave pyrrole...
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By: Dr. Jie Jack Li, Vice President of Discovery Chemistry at ChemPartner Gileadʹs antiviral drug remdesivir (Veklury) was approved by the FDA on May 1, 2020 for emergency use in coronavirus disease-2019 (COVID-19) patients after a one-day review. It took the Japanese government much longer to give the nod, seven days, before granting its regulatory approval. But one wonders: how was remdesivir discovered? Its genesis retraces back to the first antiviral drug, idoxuridine. Inspired by George H. Hitchings (Nobel laureate in 1988 for Physiology and Medicines), who started to systemically investigate purine and pyrimidine analogs as potential drugs, Professor William H. Prusoff at Yale discovered idoxuridine (IdU) as the first small-molecule antiviral drug in 1959. He is now known as the godfather of modern antiviral chemotherapy. Although IdU is too toxic to be given systemically, it is applied topically to treat eye and skin infection caused by herpes simplex virus (HSV). While its mechanism of action (MoA) is not completely elucidated, it is most likely phosphated first by kinases in both virus and normal cells to the corresponding nucleotide monophosphate (when a phosphate is attached to a nucleoside, it becomes a nucleotide), nucleotide diphosphate, and nucleoside triphosphate (NTP) sequentially. NTP is the active drug with two fates. On the one hand, when interacting with viral DNA polymerase, it terminates DNA replication and exerts antiviral activities. On the other hand, when interacting with cellular DNA polymerases, cytotoxicity, mitochondial toxicity, and antitumor activity ensued. The emergence of IdU opened a floodgate of ribonucleoside antiviral drugs. It was followed by trifluorothymidine (TFT, Viroptic), ethyldeoxyuridine (EdU), bromovinyldeoxyuridine (BVDU), and more recently, telbivudine (Tyzeka), a synthetic thymidine nucleoside analog put on the market by Novartis in 2006. Gertrude “Trudy” Elion, who shared the 1988 Nobel Prize with George Hitchings, led a team at Wellcome Research...
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By: Dr. Jie Jack Li, Vice President of Discovery Chemistry at ChemPartner Gileadʹs antiviral drug remdesivir has been catapulted to the limelight as the only FDA-approved treatment of coronavirus Covid-19 for emergency use thus far. On April 29, 2020, preliminary clinical trials indicated that the drug has shown some efficacy. While mortality rate for patients taking remdesivir is 8%, the control groupʹs mortality rate is 11%. More meaningfully, it took 11 days for patients taking remdesivir to recover while it took 15 days for patients on placebo. Finally, remdesivir is the first ray of sunshine in the dark clouds casted by the deadly invisible coronavirus. It took merely one day for the FDA to make a decision: on May 1, 2020, the FDA authorized remdesivir for emergency use in COVID-19 patients. But one wonders: how does remdesivir work? Remdesivir1, a bioisostere of natural N-nucleosides such as adenosine and guanosine, is a C-nucleoside antiviral drug, which works as an antimetabolite and blocks the synthesis of viral DNA. There are four DNA bases: adenine, guanine, thymine, and cytosine. Another base, uracil, is only seen in RNAs. Remdesivirʹs1 pyrrolotriazine fragment bears a striking resemblance to adenine and guanine. Therefore, pyrrolotriazine can serve as a bioisostere of those two bases required for the synthesis of viral DNAs. The discovery of remdesivir (GS-57341) took a long and winding route. Initially discovered as a treatment of Ebola virus (EBOV) 1, it evolved from GS-66202, the first C-nucleoside HCV polymerase inhibitor with demonstrated antiviral response in HCV-infected patients.2 C-Nucleosides have the potential for improved metabolism and pharmacokinetic properties over their natural N-nucleoside counterparts due to the presence of a strong carbon–carbon glycosidic bond and a non-natural heterocyclic base. How does remdesivir1 work as an antiviral drug? Well, it is a long story…… In terms of mechanism of...
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By: Dr. Manny Ventura, Director and Global Head of Analytical Chemistry at ChemPartner Supercritical fluid chromatography (SFC) is now a well-established tool incorporated into the small molecule drug development strategy for organizations of all types and sizes. Its imprint is almost surely on the history of development of any new advanced chiral drug candidate. Big pharmaceutical companies have been utilizing SFC for over 20 years, and most have established operations dedicated to chiral SFC separation for well over 10 years. These include analysis systems used for method development to determine the chiral purity of API’s and intermediates as well as for scaling up to purification methods. SFC preparative instruments may be utilized for low milligram scale separations up to multiple kilograms. SFC has moved past HPLC in utilization for pharmaceutical chiral analysis and purification based on several speed advantages inherent to the technology. The usual mobile phase in SFC consists primarily of CO2 plus an organic alcohol solvent compressed and mixed by a liquid/CO2 binary pump. The most fundamental advantage of this methodology is its higher optimal linear velocity. It has been shown that, for packed columns of equivalent particle size, SFC can allow flow rates three to five times higher than HPLC. With higher operating flow rates, the inherently lower viscosity of SFC mobile phases results in a lower pressure drop across the column, allowing the use of longer columns when required. Fast equilibration allows for shorter cycle times with gradient SFC separations, further reducing the time required for chiral method development. These properties yield higher efficiency separations in less time, leading to faster access to optimal methods and the ability to explore an ever-increasing number of commercial stationary phases. These advantages and others extend to chiral preparative SFC. A reduced injection-to-injection cycle time results from the higher speed...
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By: Dr. Kevin Greenman, Principal Scientist at ChemPartner When it comes to finding new chemical matter to engage biological targets, fragment-based screening (FBS) offers a number of advantages over traditional high-throughput screening (HTS). The success of this approach has resulted in a growing list of molecules advancing through clinical trials. From the perspective of a medicinal chemist, FBS makes it much faster to identify actionable hits as compared to plowing through the dross of a HTS campaign. The resulting leads tend to be of higher quality, exhibiting lower lipophilicity and lower molecular weight. The operational advantages of FBS make it particularly attractive, as a wider swath of chemical space can be searched more quickly, with fewer compounds, less protein consumption, and lower overall cost. Using the appropriate combination of biophysical and biochemical methods streamlines the validation process by removing possible artifacts at an early stage. The availability of multiple screening methods is another consideration in choosing an FBS approach. As the most widespread approach, screening by NMR is a highly effective and versatile tool for identifying fragment hits. Even within the NMR paradigm, different detection methods (e.g. CPMG, STD, waterLOGSY) are susceptible to different artifacts such that the intersection of hit sets identifies true hits with high confidence.  Other methods, such as MST, DSF and SPR; are commonly used both as primary screening tools and as downstream validation methods. Ideally, one chooses a workflow where initially identified hits are subsequently validated by a completely orthogonal technique. In my experience, the most successful embodiment is a NMR screen with follow-up by SPR. In applying FBS at ChemPartner, we provide discovery tools that can integrate with the existing strengths and capabilities of our partners. A key component of the FBS toolset is the fragment library.  We built a fragment library using a...
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By: Dr. Shireen Khan, Senior Director of Biologics at ChemPartner Through our partnership with single cell technology company Berkeley Lights, Inc., ChemPartner offers the innovative Optofluidic based Beacon® platform at our South San Francisco lab. The nano chip technology of the  Beacon® platform enables  functional characterization of  antibodies secreted from single B cells. The Berkeley Lights technology offers the opportunity for an accelerated antibody discovery workflow compared to the standard hybridoma approach.   Using the Beacon® platform, we  screened thousands of  single plasma B cells to identify unique antibodies against PD-L1.  We  immunized Balb/c mice with recombinant Fc fusion of human PD-L1 extracellular domain (ECD) and isolated CD138+ plasma B cells from bone marrow and spleen from an 8 week immunization. Plasma B cells from both spleen and bone marrow where penned as single cells onto OptoSelectTM chips for analysis.  A series of assays were performed in tandem including bead-based binding assays, cell-based binding to CHOK1 cells engineered to over-express human PD-L1, and cell-based blocking assays using PD-1. This series of assays on the Beacon enabled identification of roughly 250 antibodies binding to PD-L1, and nearly 20% of them blocked binding of PD-1 to PD-L1 on cells.  Interestingly, a majority of PD-L1 specific blocking antibodies were identified from plasma B cells isolated from bone marrow even though the yield of plasma B cells from bone marrow was less than 20% of what was obtained from the spleen.  Single plasma B cells were exported by the Beacon® for antibody sequence recovery. After reverse-transcription, amplification, and single plasma B cell sequencing by NGS, we evaluated the sequence diversity of anti-PD-L1 antibody hits, most of which were divergent across multiple residues in CDR3.  After evaluating over 30,000 single plasma B cells, we identified over 40 cell based binding and blocking antibodies that are...
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