Chemistry, Biochemistry & Physics Projects
A Comprehensive Computational Modeling of Natural Bioenhancing Agents Docked to Transport Proteins to Enhance Bioavailability
The effects of natural bioenhancers were studied on various proteins. We hypothesized that piperine would have the best effect on all the eight proteins we studied in comparison to all the other ones because it has the best bioavailability. Bioavailability is the amount of drug that is absorbed in order for it to have an active effect. Along with this, piperine has had the ability to increase the bioavailability of different drugs from 30% to 200%. The molecular structure of piperine allows for enzyme inhibition, which thus increases the bioavailability.
Tanusree Banerjee, Destiny Pinto, Tejasvi Hariharan, Avi Uppalapati, Via Das, Riya Ubale, Shalini Singh
A Stability Study of Torula Yeast RNA, with Applications in Drug Delivery
In being an unstable, typically single-stranded molecule, RNA plays a variety of roles within the genome. Through its unique properties of binding, condensation, gene interference, and genome alteration, the nucleic acid has been considered to be a molecule with great clinical potential. RNA stability and condensation, as the focus of this project, were investigated with the goal of improving clinical drug delivery via cytoplasmic transport, specifically in how the nucleic acid’s capabilities for compaction can be leveraged as a delivery vehicle. RNase, or ribonuclease, a group of enzymes responsible for RNA degradation, is present in an abundance of environments and was the primary method used for RNA degradation in the form of fetal bovine serum and pure ribonuclease A. Primary degradation assays were tested for the potential of calcium phosphate as a viable protective nanoparticle in which the susceptible RNA sample can be enveloped. RNA was bound in TBE buffer with 1% fetal bovine serum simulating in vivo environments with intense ribonuclease presence. To streamline the analysis of CaP-bound RNA following degradation, various pH, time, extraction salt, and buffer conditions were experimented with to improve the efficiency of RNA elution off the nanoparticle. Through experimentation, the optimal extraction conditions gave 0.7 mg/mL of RNA (originally 5 mg/mL) using 1M NaCl, a pH of 10, and an incubation period of 1 week. In more basic pHs, longer incubation periods are found to have increased the amount of RNA eluted from calcium phosphate. In further experimentation, the calcium phosphate nanoparticle will be utilized to facilitate RNA compaction in order to encapsulate the nucleic acid within delivery vehicles, such as liposomes or lipid nanoparticles.
Analyzing MTT assays and qRT-PCR to gain insight into biological mechanism of action of andrographolide and analogs
Derived from Andrographis paniculata, andrographolide is a natural product that has been investigated as a therapeutic lead for prominent diseases such as colorectal cancer and multiple sclerosis by inhibiting the Nf-kB transcription factor, which interferes with key cell signaling pathways involved with cell metastasis and tumor survival. The semisynthesis of andrographolide by altering the C-ring butenolide and A/B ring trans-decalin yields more analogs with improved tolerability, selectivity, and potency. To test the biological effects of these compounds, MTT biochemical assays were conducted to determine the in-vitro cytotoxicity in Chinese hamster ovary (CHO) cells. The reduction of the yellow tetrazolium salt (5-diphenyl tetrazolium bromide) to insoluble, purple formazan crystals by the metabolically active cells thus serves as colorimetric detection to observe the cellular activity of treated cells. In addition to cytotoxicity assays, we used real-time quantitative polymerase chain reaction (qRT-PCR) to create a gene expression assay. By screening for genes that fall under the MAPK, Nf-kB, and mTOR cell signaling pathways, qRT-PCR can provide us an accurate image of what genes are directly affected by andrographolide which can then provide insight on the compound’s exact effects on biological activity.
Vivian Long, Trisha Krishnarajpet, Aditi Putrevu
Analyzing and Optimizing the Molecular Interactions of Emodin for Protein Inhibition and Drug Delivery
Emodin, a potent anticancer agent derived from natural plants, possesses a unique structure that consists of an aromatic core surrounded by polar moieties. Consequently, it is able to interact with moderately polar regions, which include the active sites of serine/threonine kinases and polymers like chitosan. Serine/threonine kinases are involved in promoting cancer growth; therefore, inhibiting them with emodin can reduce cancer cell proliferation. We proved that emodin could bind to a variety of serine/threonine kinases through hydrophobic interactions and hydrogen bonding, making it an ideal scaffold compound in drug design. Through molecular dynamics, emodin was found to bind the most strongly to MAPK-9, confirming that emodin competitively inhibits the ATP binding region of the kinase. Furthermore, emodin was also able to interact with chitosan, which lays a framework to investigate its incorporation into chitosan nanoparticles. Its entrapment efficiency was predicted with molecular dynamics, but we found that it did not account for all the chemical components in chitosan nanoparticles. Despite this, emodin is poorly soluble in water, which poses a difficulty to the traditional method employed to synthesize chitosan nanoparticles through ionic gelation. Therefore, we optimized a nanoparticle synthesis method to successfully entrap emodin with relatively high entrapment efficiencies. Hence, we have demonstrated that emodin’s unique structure allows it to inhibit proteins of anticancer relevance as well as an ideal candidate for drug nanodelivery systems.
Rohit Suresh, Sahana Kuchibhotla , Srinitya Sriram, Yash Kamdar, Vivek Garg, Arshiya Anand
Antibody Drug conjugate linker technology
Although several other activation methods of prodrugs have been designed and evaluated, photorelease shows immense potential due to its increased bioorthogonality and ease of control. Here, we present an in-depth study to improve prodrug photoreleasability and its biological implications. We began by examining the effect of aromatically substituted electron withdrawing and electron donating moieties on the photorelease kinetics of an ortho-nitrobenzyl carbonate group. In addition, we explored the impact of a benzylic deuterium substitution to determine if kinetic isotope effect (KIE) accomunts for accelerated photorelease rates. However, a drawback of the o-nitrobenzyl group stems from the necessity of UV activation, which damages healthy tissue cells. To address this, we synthesized a biphenyl system in which we added aromatic conjugation to the nitrobenzene via a palladium-catalyzed cross-coupling in order to reduce required photon energy levels, thereby redshifting the photon trigger. The mechanistic insights derived from the initial photorelease assays were then applied towards the prodrugging of podophyllotoxin, a potent chemotherapeutic small molecule drug, in order to increase its pharmaceutical potential. Ultimately, the compatibility of such photoreleasable groups with targeted drug delivery systems was revealed through the development of a novel photoreleasable antibody-drug conjugate.
Harsha Rajkumar, Gavin Li
Benchtop 19F nuclear magnetic resonance spectroscopy enabled kinetic studies and reaction optimization of the synthesis of carmofur and related 5-fluorouracil analogs
Carmofur, a prodrug derivative of 5-fluorouracil (5-FU), was initially developed as an antineoplastic agent used in the treatment of colorectal and other cancers by acid ceramide-induced apoptosis. Recent drug repurposing efforts have identified carmofur as a covalent inhibitor of the SARS-CoV-2 main protease. This SARS-CoV-2 main protease (Mpro) plays an essential role in the processing of the polyproteins that are translated from the viral RNA, therefore making it an attractive drug target for the treatment of COVID-19. Here, we present the in silico evaluation and synthesis of carmofur and a library of related 5-fluorouracil analogs with aliphatic, amino acid, and aromatic fragments against mutations in Mpro. Furthermore, carmofur’s 5-FU head serves as a spectroscopic handle for benchtop 19F nuclear magnetic resonance spectroscopy (NMR). Recent advances in benchtop NMR has facilitated real-time monitoring, characterization, and quantification of chemical entities without the use of financially prohibitive deuterated solvents, and provides the opportunity to rapidly and quantitatively optimize reaction conditions that conventional reaction tracking methods cannot produce. Here, we implement benchtop 19F NMR as a practical analytical tool to track the reaction kinetics of 5-FU with various isocyanates, and optimize reaction conditions to synthesize carmofur and its analogs on-scale for future in vivo biological testing.
Xina Wang, Amber Lu, Kavya Pandrangi, Lexi Xu, Breanna Lu, Theodore Khow, Erika Yu
Benchtop nuclear magnetic resonance spectroscopy provides mechanistic insight into the Biginelli condensation towards the synthesis of novel trifluorinated pyrimidine compounds as antiproliferative agents
The Biginelli cyclocondensation is a multicomponent reaction used to synthesize dihydropyrimidines by utilizing ethyl acetoacetate, thiourea, and an aryl aldehyde under acidic conditions. In this study, 19F NMR spectroscopy was utilized to monitor the synthesis of novel trifluorinated analogs of monastrol, a small molecule kinesin Eg5 inhibitor, and to probe the mechanistic pathways of the Biginelli cyclocondensation. Through the use of 19F NMR time course kinetic experiments with trifluoro toluene as an internal standard, we identified an unknown reactive intermediate, suggesting that the trifluorinated analogues of monastrol proceeded through a different operative mechanism. By analyzing the kinetics’ experimental data, we were also able to derive Hammett linear free energy relationships (LFER) to determine stereoelectronic effects of para- and meta- substituted aryl aldehydes to corresponding reaction rates and mechanistic routes. Here, we present discoveries regarding the application of benchtop 1H and 19F NMR spectroscopy to characterize reactive intermediates and mechanistically probe reaction pathways.
Beta Lactam, Prodrugs, Machine Learning for Drug Discovery, Eugenol, Chemical Neuroscience, Metal Catalysis, COVID/Carmofur
Varies based on project/subgroup
Varies based on project/subgroup
Biological Evaluation and In-silico Screening of a Novel Library of Eugenol Analogs as Potential Antimicrobial Ligands
Eugenol is naturally occuring allylbenzene small molecule found primarily in clove oil, as well as the oils of numerous other plants. It has been proven to have numerous biological properties, including as an antimicrobial, anti fungal, and neuroactive agent. It’s also widely used in the cosmetics and food industries. We synthesized a library of novel eugenol analogs to test it’s potent biological efficacy against bacteria and fungi. In addition, we did in-silico screens of the the compounds against receptors that contribute to epilepsy and seizing activity in humans. The effects of our analogs on these biological targets is unknown, so we compare the effectiveness of our compounds against the natural molecules.
Aashi Shah Charissa Luk Udbhav Avadhani Tiffany Wang Shamita Bhattacharjee Alivia Zhang
Chemical Synthesis and Ex-Vivo Evaluation of Berberine Analogs as DNA-Binding Singlet Oxygen Photosensitizers and Anti-Bacterial Drugs
Berberine, a natural product isoquinoline alkaloid, has been shown to exert its biological activity through in situ production of singlet oxygen, a highly reactive oxygen species, upon irradiation. Its putative mechanism of action as a DNA-binding singlet oxygen photosensitizer stems from its electronic structure, wherein upon irradiation, it sensitizes triplet oxygen to singlet oxygen to incur irreversible DNA damage, resulting in apoptosis. Through semisynthetic modifications of the berberine scaffold, we were able to modulate berberine’s electronic structure towards bolstering its photosensitizing properties. Regioselective modifications, such as grignard additions to C8 and demethylation and cross couplings to C9, enabled the generation of a library of berberine analogues. Here, we present two ex-vivo experiments towards evaluating the DNA-binding singlet oxygen photosensitizing abilities of Berberine and related analogues. Through the use of a hetero Diels-Alder reaction between singlet oxygen and a terpene, we were able to quantitatively monitor singlet oxygen production with benchtop NMR. Moreover, we used HPLC in conjunction with in silico methods towards the construction of a structure activity relationship between berberine and various DNA structures.
Chemical synthesis and Hammett LFER-controlled hydrolytic stability of a library of A-ring diversified Andrographolide analogs for controlled release and delivery
Andrographolide, a labdane diterpenoid extracted from the Ayurvedic plant andrographis paniculata, exerts its biological activity through the inhibition of NF-κB, a protein transcription factor that plays a role in atherosclerotic pathogenesis. This natural product is currently in clinical trials for HIV/AIDs and multiple sclerosis. To begin, we synthesized a compound called 3,19-isopropylidene andrographolide (“acetonide”) with an acetonide group installed on the A/B trans-decalin system. However, ketals have been known to decrease the stability of compounds because of their ability to hydrolyze in basic and slightly acidic conditions. Since acetonide performs better than andrographolide in biological assays, we wanted to probe the question if acetonide was an analog or a prodrug. We turned to high-performance liquid chromatography (HPLC) to design a method that would track the rate of hydrolysis of acetonide back into the natural product. To exert complete control over the rate of hydrolysis, we designed a library of benzaldehyde acetal prodrugs that used different substituents on the para and meta position of the benzaldehyde. We postulate that Hammett Linear Free Energy Relationships, or the correlation between an aryl aldehyde and its willingness to give up an electron, will play a role in the rate of hydrolysis. Through our work, we hope to create a better delivery system of andrographolide to increase efficiency and potency in biological systems.
Shreya Somani, Carina Zhou
Comparative singlet oxygen photosensitizer efficiency of berberine, rose bengal, and methylene blue by time course nuclear magnetic resonance (NMR) monitoring of a photochemical 4+2 cycloaddition endoperoxide formation
Berberine, a natural product alkaloid, has been shown to exert biological activity via in situ production of singlet oxygen, a highly reactive oxygen species, when photo irradiated. Berberine utilizes singlet oxygen in its putative mechanism of action, wherein it forms an activated complex with DNA and photosensitizes triplet oxygen to singlet oxygen to specifically oxidize guanine residues, halting cell replication, leading to cell death. This has potential application in photodynamic therapy, alongside other such compounds which also act as photosensitizers and produce singlet oxygen in situ. The quantification of singlet oxygen in various photosensitizers, including berberine, is essential for determining their photosensitizer efficiencies. We hypothesized that the singlet oxygen produced by photoirradiation of berberine would be superior to the aforementioned photosensitizers when irradiated with UV light, but inferior under visible light conditions, due to its strong absorbance of UV wavelengths. Here, we report the usage of time course 1H nuclear magnetic resonance (NMR) spectroscopy to trap singlet oxygen via a 4+2 cycloaddition with terpinene, as well as theoretical calculations by time-dependent density functional theory (TD-DFT) towards quantification berberine's singlet oxygen production against two known photosensitizers, methylene blue and rose bengal, to determine berberine’s efficacy as a singlet oxygen photosensitizer. We envision that similar processes can be utilized for the evaluation of berberine analogs or other photosensitizing agents, and the identification of other potential medicinally significant singlet oxygen photosensitizers.
Sarah Su, Karthikha Sri Indran, Sohie Pal, Emma Le, Anika Regan, Meher Jain, Aashi Shah , David Iglesias, Andrew Wang
Developing a Split-GFP Assay to Quantify the Endosomal Escape of Nanoparticles
The clinical use of drug carrying nanoparticles has been expanding and even used in the COVID mRNA vaccine. However, their limitations lie in their low endosomal escape efficiency. There are many different nanomaterials and endosomal escape domains that improve transfection, yet there isn’t a method to actually quantify and compare their endosomal escape capabilities. Our project offers a quantitative assay method for endosomal escape efficiency, using the delivery of GFP11 into GFP1-10 expressing cells and analyzing the fluorescence of their reconstitution. We will test their assay ability using Calcium phosphate nanoparticles (CaP): a promising non cytotoxic and versatile delivery vector. CaP can hold macromolecules such as nucleic acids and proteins with ionic surface charges and we plan to take advantage of this to deliver GFP11 through the endosomal escape route with cell penetrating peptides. With this, we aim to provide practical applications of our assay to enhance and research CaP’s potential as a high-efficiency drug delivery vector.
Development of next-generation prodrugging strategies - molecular solutions to clinical problems
The toxicity of small molecule drugs employed in chemotherapy introduces a myriad of risks that pose harm to the long term health of patients. Side effects such as hair loss, internal bleeding and even loss of appetite can all be attributed to the off target toxicity of chemo agents. In light of this, researchers have studied prodrugs and biomolecule drug conjugates in hopes to alleviate such symptoms. One type of biomolecule drug conjugate are antibody drug conjugates (ADC's). Antibody-drug conjugates (ADCs), a novel class of immunotherapeutics, have gained traction due to their highly specific delivery of cytotoxic payloads to tumor sites. Utilizing routes developed by Michel et. al (2020), our lab synthesized SN-38 drug conjugates and attached them to multiple antibodies for in-vitro testing. In addition, photorelease has shown immense potential due to its increased bio-orthogonality and ease of control. Using a novel two-step synthetic route, our lab developed three photoreleasble prodrugs of podophyllotoxin.
Harsha Rajkumar, Tyler Dee, Gavin Li, Claire Song, Ishan patel, Alyssa Kim, Lorelei Xia, Lexi Xu, Sanjana Vadapalli, Zachary Bashkin
EGCG and Ascorbic Acid Nanoparticles against HCT 116 cell lines
This project focuses on conjugating EGCG and ascorbic acid to make nanoparticles that combat colon cancer. EGCG, or Epigallocatechin, is a major polyphenol in green tea, and is a catechin. It has anti-inflammatory and antioxidant properties. It has been previously found that EGCG prohibits tumor growth. However, EGCG has low bioavailability, meaning that it isn’t readily usable by the body. To increase the bioavailability, ascorbic acid, or Vitamin C, is being used. Ascorbic acid (AA), or Vitamin C, significantly decreases the growth of cancer cells and can help strengthen the immune system. We are also using PLGA (poly lactic-co-glycolic acid) with 5.25% PEG content as a polymer that encapsulates the two drugs (EGCG and AA) in our nanoparticles. PLGA has been used for drug delivery in the past, so incorporating PLGA in the EGCG and AA conjugated nanoparticles will help with the drug release. We are creating the nanoparticles using the nanoprecipitation method. We aim to calculate the entrapment efficiency and release rate of the nanoparticles, and then test their effectiveness on HCT116 cells.
Meera Iyer, Aarya Morgaonkar, Simran Tawari, Rose Liu , Dalia Jazrawi, Amra Abid
G-Quad Stabilization with Indole-Based Dyes
The G-quadruplex (G4) is formed in nucleic acids by guanine-rich DNA sequences and is commonly researched in the development of cancer treatments. Dyes such as isatin, indigo, and azo dyes are a promising novel area of research in terms of G4 stabilization, providing a possible non-cytotoxic chemotherapy substitute by stunting cancer growth by inhibiting the reverse transcriptase hTERT. The large planar aromatic surface of the G4 is a promising rationale for the binding of cyclic, planar ligands with aromatic characteristics of dye and indole-based ligands. Our research suggests that contrary to previous research, intercalative binding plays a very small role in binding specificity. We developed indole-based ligands that effectively bind to and stabilize the G4’s activity. Our research found that smaller drugs required binding to the phosphate backbones of the G4 for thermodynamic favorability, but that larger molecules were generally favorable with higher observed binding affinities. Smaller ligands pursued a different pathway of stabilization than more traditional ligands by binding to the formed grooves characterized in the G4’s helical structure, making heavy use of polar interactions. The favorability of larger molecules was mostly attributed to pi-pi stacking with the endplate and interactions with the central cations; larger molecules needed to achieve a certain amount of curvature in order to successfully bind to the grooves in the G4.
Anna Han, Ananya Suryadevara, Sriya Gonuguntla Sankrith Ramani, Isha Tailor
High throughput screening and chemical synthesis of novel non-nucleoside reverse transcriptase inhibitors (NNRTI’s) enable the discovery of novel antivirals and therapeutics for HIV/AIDS
Efavirenz is a synthetic FDA-approved non-nucleoside reverse transcriptase inhibitor (NNRTI) that has been demonstrated to bind to the allosteric binding pocket of reverse transcriptase (RT) of the human immunodeficiency virus (HIV), effectively inhibiting viral replication. However, the emergence of new drug-resistant variants has reduced the effectiveness of NNRTIs, necessitating the synthesis of new compounds with better biological profiles. Analogs of efavirenz hold potential as next-generation NNRTIs and may overcome resistance to the rapidly mutating HIV RT. In this study, we utilize high-throughput virtual screening (HTVS) to evaluate 112 efavirenz analogs in silico with cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, phenyl, tert butyl, and methyl groups as well as chlorine, fluorine, methyl, and trifluoromethyl rotated around the 3, 4, 5, 6 positions on the benzene ring in the efavirenz scaffold. Analogs were evaluated against the wild-type (WT) RT as well as efavirenz-resistant mutations in the WT HIV protein to determine several hit compounds as potential next-generation NNRTIs. In addition, we are currently investigating the synthesis of efavirenz itself using catalytic asymmetric alkynylation of trifluoromethyl ketones as an alternative to the current not atom efficient Merck synthesis.
Shelley Li, Kavya Pandrangi, Anushree Marimuthu, Anjali Prabhu, Madi Lloyd, Nandika Nambiar, Alice Finkelstein
Hypoglycemic activity of Trigonella foenum-graecum in the C. elegans model
Diabetes Mellitus is a high-risk chronic metabolic disease and is the seventh leading cause of death in the United States. There are several types of diabetes mellitus, including type 1 DM, type 2 DM, maturity-onset diabetes of the young, and gestational diabetes. Insulin is a key hormone that converts glucose to energy. Because of the lack of insulin production, cells are unable to use glucose in order to produce energy, resulting in hyperglycemia. Even though diabetes is one of the oldest diseases, no cure has been discovered; however, several drugs have been developed to manage it more effectively. Recently, natural products are becoming a major part of the pharmaceutical drug industry, and are widely used especially in the east. Trigonella foenum-graecum, or fenugreek, is one of these drugs. Fenugreek is a medicinal plant known to have antidiabetic properties which stem from its bioactive compounds like diosgenin, trigonelline, 4-hydroxyisoleucine, leucine, and L-lysine. Our research is focused on determining the most efficient method in which different phytoconstituents can be extracted, conduct total content assays and assess their anti-diabetic potential and chemical properties.
In silico screen and 19F nuclear magnetic resonance spectroscopy enabled chemical synthesis of a library of carmofur analogs as potential inhibitors of the SARS-CoV-2 main protease (Mpro)
Carmofur, a 5-fluorouracil derivative, was initially developed as an antineoplastic agent that inhibits acid ceramidase and tested for its efficacy on colorectal cancer cell lines. More recently, through drug repurposing efforts, it has been identified as a covalent inhibitor of the main protease of SARS-CoV-2. This SARS-CoV-2 main protease (Mpro) plays an essential role in the processing of the polyproteins that are translated from the viral RNA, therefore making it an attractive drug target for the treatment of COVID-19. Here, we present the in silico evaluation and synthesis of carmofur and a library of related 5-fluorouracil analogs with aliphatic, amino acid, and aromatic fragments against mutations in Mpro. Homology modeling was used to determine the interactions between carmofur analogs and Mpro as a result of the mutations and their effects on the binding affinity of our analogs, revealing potential hit compounds to further develop for combating COVID-19. Furthermore, using the 5-fluorinated position as a handle, benchtop 19F nuclear magnetic resonance spectroscopy (NMR) has enabled the real-time quantitative monitoring and scalable synthesis of novel 5-fluorouracil analogs as potentially more effective inhibitors.
Xina Wang, Julia Vu, Charissa Luk, Neha Mandava, Udbhav Avadhani, Kavya Pandrangi , Aishi Rao , Jane Wu, Emma Le, Anushka Peer
Green synthesis, using plant extracts, is rapidly emerging as a more commonly used method and a safe alternative to the chemical synthesis of metal nanoparticles. Through green synthesizing methods, we anticipate discovering how nanoparticles can pass the blood-brain barrier and enter the central nervous system to provide therapeutics, inhibitors, or other types of drug delivery to the central nervous system. In our study, we synthesized two types of metal nanoparticles, iron oxide and zinc oxide using an eco-friendly method. Iron oxide nanoparticles were synthesized using Coriandrum sativum (cilantro) leaf extract and ferrous sulfate heptahydrate salt. Zinc oxide nanoparticles were synthesized using L. Nobilis (bay leaf) extract and zinc nitrate salt. The synthesized metal nanoparticles were then characterized using Fourier Transform Infrared Spectroscopy (FT-IR) and Ultraviolet-Visible Spectroscopy (UV-Vis). An FT- IR was done to measure the absorbance bands while the UV-Vis was done to measure the levels of absorbance. Our further plans include testing drug delivery potential by introducing ZnO and FeO into the CNS through the BBB to measure its effectiveness and synthesizing the nanoparticles by using elements of an anti-inflammatory compound to observe its significance. Ultimately, the goal of this project is to discover a method to treat neurodegenerative diseases.
Morgan Chan, Reeva Randeri, Abhiraj Bhashkar, Dhruv Sastry, Alpita Balu
Modification of surface tension of a green solvent to enhance graphene synthesis
Graphene is an allotrope of carbon, the single atomic layer of graphite. With a unique hexagonal structure of tightly latticed carbon atoms and sp2 hybridization, graphene presents a multitude of properties beneficial to the future of material science. Among them, our group focuses on graphene’s incredible strength, high conductivity, and lightweight structure. These properties make graphene a strong candidate for electrode construction in supercapacitors. Our goal is to find a scalable, green, and efficient method to synthesize graphene. Some existing methods include mechanical exfoliation, epitaxial growth, and pyrolysis. These processes are costly, not scalable, and/or have a tendency to produce graphene sheets with imperfections. However, synthesis through liquid-phase exfoliation shows promise. Our research focused on the comparison between bath and probe sonication, as well as the use of different solvents to help enhance exfoliation. We tested different sonicating durations per method; 3, 6, 9, and 12 hours. Literature indicates that different solvents help increase graphene yield. Solvents with the right surface tension will boost exfoliation. The solvents we tested include an ethanol and water mixture, coconut water, curcumin water, and hand/dish soap. Previous research has shown ethanol and water to be an effective solvent, due to the solvent’s similar surface tension to that of graphene. Current investigations are being carried out on coconut water, curcumin water, and hand/dish soap. Coconut water is an antioxidant, and can be used to derive graphene from graphite oxide. Curcumin has properties that can increase yield. Hand and dish soap include surfactants that can enhance exfoliation. For each test we prepared ink using the derived graphene, executing UV-Vis and FTIR spectroscopy for characterization of impurities. We also carried out cyclic voltammetry to test for capacitance. We aim to continue investigating other solvents, to find which characteristics are most efficient in graphene synthesis. We also plan to explore other methods of synthesis outside of liquid-phase exfoliation, such as magnetic separation. Finding a scalable, cost-effective and efficient method of green graphene synthesis that is feasible will be a great advantage to the supercapacitor electrode industry, paving the way to more efficient and long-term storage of energy.
Tze Tseng Soh,
Modular mimics of neuroactive alkaloids: design, synthesis, cholinesterase inhibitory activity, and sterics study of novel rivastigmine analogs
For centuries, neuroactive alkaloids isolated from naturally occurring phytochemical sources have been crucial in the identification and optimization of small molecules with potency in treating neurological disorders. While some of these compounds have gone on to clinical use themselves, others have inspired the development of synthetic analogs, which might possess greater potency or better pharmacological features than the natural product itself. One such naturally occurring alkaloid, physostigmine, which is found in the calabar bean plant Physostigma venenosum, has been demonstrated to be a potent cholinesterase inhibitor. However, some of physostigmine's characteristics limit its therapeutic potential, prompting the development of its synthetic counterpart, rivastigmine. The research in our group focused on the synthetic optimization of rivastigmine and its analogs, utilizing computer modeling and biological assays to determine the most favorable analog for inhibition of acetylcholinesterase (AChE). Through such studies, it was determined that rivastigmine and its analogs were less effective at inhibiting AChE than physostigmine, and their biological activity is governed by sterics, prompting us to pursue three routes: the synthesis of S-enantiopure versions of our analogs, the synthesis of analogs with less steric hindrance, and the study of biological activity for all analogs on both cholinesterase enzymes to determine enzyme selectivity.
Erika Yu, Shloka Raghavan, Harrison Xu, Niharika Nambiar, Bridget Liu, Adrienne Ferguson, Sripradha Manikantan, Alice Finkelstein, Xina Wang
Natural Product Polyphenol Inhibition of Amyloid-Beta Aggregation
Neurodegenerative diseases, including Alzheimer’s, have long been the focal point of modern research. Till date, it has been proven that there is a direct correlation between β-amyloid protein aggregation and uncontrolled neural cell apoptosis, preludial to a majority of Alzheimer’s symptoms. A potential preventative and curative therapy to Alzheimer’s and related neurodegenerative diseases could be based on the inhibition of said β-amyloid and related prion proteins aggregation. Polyphenols are naturally occurring organic molecules that consist of one or more aromatic phenolic rings. Our research is meant to yield the most effective natural product polyphenols in said inhibition. Our in silico research assessed a large range of natural product polyphenol candidates and their potential to interact favorably with targeted proteins through docking softwares. Our in vitro and in vivo work continued testing on select polyphenols with the highest binding affinities using the model organism C elegans.
Varsha Beldona, Ayush Patel, Kavya Patel, Neha Abraham, Alyssa Halvorsen, Ashlee Liu, Nandini Mannem
Photorelease kinetics of aryl-substituted o-nitrobenzyl prodrug linkers towards reactivity-guided design of next-generation prodrugs
Photocleavable prodrugs include photoreactive linkers and substitutions sensitive to visible light, UV light, and LED lights. Being able to activate prodrugs using photoreactivity would allow for non-invasive and efficient procedures to specifically target drug activation in localized areas. One specific goal being that of bio-orthogonality, a function in which photochemical triggers have been able to adopt, specifically the o-nitrobenzyl linker. The use of this orthogonal linker dates as far back as the 1970s with its photo-cleaving mechanism and resulting products having been heavily studied. Due to the high prevalence of o-nitrobenzyl linker derivatives being used for the study of biological processes, our research focuses on studying the photo-release kinetics of ortho-nitrobenzyl ester compounds by monitoring the effects of various aromatic substitutions. In this study, we examined the effect of 6 different aryl-substituted o-nitrobenzyl linkers to test the effect of electron-donating and electron-withdrawing groups on its photo-cleaving ability. The properties of our o-nitrobenzyl-based novel synthetic derivatives were investigated by means of 1H NMR, 13C NMR, IR-spectroscopy, TD-DFT, and GC-MS methods. Moreover, to address applications within the field of anti-cancer therapeutics, semi-synthesis of a 2-nitrobenzyl podophyllotoxin prodrug is performed to elucidate photo-release properties through NMR and LC-MS methods.
Selin Kocalar, Tvisha Nepani, Aishi Rao, Alice Zhou, Harsha Rohanraj, Warren Chang, Emma Ka
Photorelease kinetics of aryl-substituted o-nitrobenzyl prodrug linkers towards reactivity-guided design of next-generation prodrugs
Photorelease kinetics of aryl-substituted o-nitrobenzyl prodrug linkers towards reactivity-guided design of next-generation prodrugs --- Photocleavable prodrugs include photoreactive linkers and substitutions sensitive to visible light, UV light, and LED lights. Being able to activate prodrugs using photoreactivity would allow for non-invasive and efficient procedures to specifically target drug activation in localized areas. One specific goal being that of bio-orthogonality, a function in which photochemical triggers have been able to adopt, specifically the o-nitrobenzyl linker. The use of this orthogonal linker dates as far back as the 1970s with its photo-cleaving mechanism and resulting products having been heavily studied. Due to the high prevalence of o-nitrobenzyl linker derivatives being used for the study of biological processes, our research focuses on studying the photo-release kinetics of ortho-nitrobenzyl ester compounds by monitoring the effects of various aromatic substitutions. In this study, we examined the effect of 6 different aryl-substituted o-nitrobenzyl linkers to test the effect of electron-donating and electron-withdrawing groups on its photo-cleaving ability. The properties of our o-nitrobenzyl-based novel synthetic derivatives were investigated by means of 1H NMR, 13C NMR, IR-spectroscopy, TD-DFT, and GC-MS methods. Moreover, to address applications within the field of anti-cancer therapeutics, semi-synthesis of a 2-nitrobenzyl podophyllotoxin prodrug is performed to elucidate photo-release properties through NMR and LC-MS methods.
Anika Regan, Selin Kocalar, Alice Zhou, Aishi Rao, Kuvam Bhatnagar, Harsha Raj, Elena Brierley Green, Shloka Raghavan
Pyrazole FTO Inhibitors; Machine Learning towards Drug Discovery
FTO: The fat-mass and obesity-associated (FTO) gene, located on human chromosome 16, codes for the FTO protein, whose expression has been positively correlated to conditions such as obesity and cardiovascular disease. The FTO protein is a homolog of the AlkB family of proteins and is known to demethylate 3-methyluracil in RNA. This purported mechanism of RNA demethylation has associated the FTO protein to metabolic and fat-mass homeostasis. As the rate of obesity continues to rise in the modern world, it is imperative that we seek to inhibit the demethylation of RNA by the FTO protein. Previous studies of the FTO protein have observed a variety of binding domains consisting of amino acids to which ligands interact through electrostatic and hydrophobic systems. Here, we report an exhaustive computational structure-activity relationship (SAR) of compounds observed to bind to and potentially inhibit the FTO protein. Both compounds that have previously been reported to inhibit the demethylation of RNA by FTO as well as novel compounds that may inhibit this mechanism were screened in silico to probe structural trends in the binding of ligands to known binding domains in the FTO protein. It was determined that the polarity and geometric structure of FTO protein inhibitors as well as the size of FTO protein cofactor affect the free energy of binding of potential FTO protein inhibitors to the FTO protein. MLDD: With advancements in the field of machine learning powered by on-demand computing and information processing at big data scale, high throughput virtual screening (HTVS) has become a more attractive method, reducing both screening costs and the timeframe from hit-to-lead for drug candidates. The efficiency of performing high throughput fingerprinting using cheminformatics based approaches coupled with machine learning to model and identify structure-activity relationships between a library of ligands and a target has immense potential to improve the time-to-market for the drug development process. In this study, we compare the accuracy of molecular descriptors from two cheminformatics software libraries, Mordred and PaDEL, in their ability to characterize the chemo-structural composition of 53 compounds from NNRTI class and a database of FDA-approved drugs targeting HIV-1 RT enzyme. A Logistic Regression model was built to classify which molecules are NNRTIs based on salient descriptors from each software. From these results, we are able to identify the structural trends present in potential inhibitors of the HIV-1 RT enzyme. The logistic regression model trained on Mordred descriptors had a 100% classification accuracy and an F1 score of 1, while the model trained on PaDEL descriptors had an accuracy of 96.7% and an F1 score of 0.9. The classification model built with the filtered set of descriptors from Modred was found to be superior to the model using PaDEL descriptors as it revealed significant cluster separation between the 53 NNRTI molecules from other drugs while the model with the filtered PaDEL descriptors did not show clear distinction between classes. The approach outlined in this work can accelerate the identification of hit compounds and improve the throughput and efficiency of the drug discovery pipeline.
FTO: Bhavesh Ashok, Danielle Hedvig, Shreya Sundar, Arun Yadavalli, Andrew Chen, Somya Talwar, Rachel Chan
MLDD: Bhavesh Ashok, Tanish Baranwal, Udbhav Avadhani, Vishak Srikanth, Geethika Biddala, Mihir Kale, Tvisha Nepani, Anya Goyal, Luqman Zaceria, Calista Lee, Srikar Kolluru, Natalia Williams, Maya Poghosyan, Megha Govindu
Brah/ Njoo/ Downing
Reactivity informed design, synthesis, and targeted delivery of andrographolide and analogs, Nf-kB regulated natural products for cancer treatment and degenerative diseases
Andrographolide, a labdane diterpenoid extracted from Andrographis paniculata, has been investigated as a therapeutic lead for many diseases. Namely, it has been found to exert its biological activity through inhibition of Nf-kB, a transcription factor at the crossroads of a myriad of cell signaling pathways, including those pertaining to tumor survival and metastasis. Synthesis of derivatives of the natural product has the potential to create analogs and prodrugs of the compound that could improve tolerability, selectivity, and potency. Here we present the synthesis of C-ring modified andrographolide analogs with altered Michael acceptor properties, as well as a series of acid hydrolyzable acetal and ketal analogs, including efforts towards an andrographolide and antibody drug conjugate (ADC) which we assay for controlled delivery and release. We use a quantitative reverse transcriptase PCR (qRT-PCR) assay as a proxy for Nf-kB regulated gene expression.
Samyukta Athreya, Srishti Venkatesan, Harrison Xu, Harsha Rajkumar, Anushree Marimuthu, Keira Chatwin, Vivian Long, Madi Lloyd, Aashi Shah, Andrew Chen, Anjali Prabhu, Lawrence Long, Yilin Fang
Strain-selective in vivo and in silico structure activity relationship (SAR) of N-acyl β-lactam broad spectrum antibiotics
β-lactam antibiotics have been used for centuries since Alexander Flemming first isolated the natural product, Penicillin G, from a fungus. As bacteria have evolved, they have started to develop resistance to these antibiotics. Therefore, continuously developing new antibiotics is important to fight bacterial resistance. Penicillin antibiotics fight bacteria by mimicking the D-Ala-D-Ala active site region of penicillin-binding proteins (PBP). PBPs are transpeptidases used in the synthesis of bacterial cell walls. New β-lactam antibiotics can be developed through the semi-synthesis of 6-aminopenicillanic acid or by synthesizing the core β-lactam ring. A Staudinger 2+2 cycloaddition can be utilized to develop novel β-lactam antibiotics with the core ring. Additionally, commercially available penicillin antibiotics can help us understand the structure-activity relationship for antibiotic efficacy. Using Kirby-Bauer assays we can understand how structure affects the antibacterial efficacy of different penicillin antibiotics. The synthesis of the β-lactam ring and penicillin-type analogs opens up the field of organic chemistry to the development of new antibiotics.
Ayeeshi Poosarla, Ria Kolala, Sohie Pal, Udbhav Avadhani, Chandraki Chatterjee, Emily Goyal, Nina Nguyen, Reha Matai, Aashika Duvoor
Synthesis and Structure-Activity Relationship of 2-Substituted Benzimidazole KRAS Inhibitors
The Kristen rat Sarcoma viral oncogene homolog (KRAS) codes for the KRAS protein, a GTPase involved in cell differentiation and proliferation. Gain-of-function mutations in the KRAS oncogene can cause constitutive activation of the KRAS GTPase, which can lead to cell proliferation and tumorigenesis. In this study, we investigate the structure-activity relationship (SAR) and druggability of a library of novel benzimidazole analogs as KRAS inhibitors. We focused on the KRAS protein that when mutated, replaces the glycine at the twelfth amino acid position with aspartic acid, shorthanded to KRAS G12D. In silico methods were used to design benzimidazoles, model protein-ligand complexes between these compounds and the KRAS G12D protein, and identify trends among atomic-level receptor-ligand interactions. A total of 297 novel benzimidazole compounds, and 232 novel benzimidazole compounds, were designed and docked to KRAS G12D, and all compounds were also screened for druggability, toxicity, and human absorption capabilities. Overall, we found that benzimidazole analogs that had high molecular weights, were hydrophobic, had low polarity, were highly polarizable, and adopted an “L” shaped structure tended to have the highest binding affinities to the KRAS G12D protein. Based on our molecular docking and druggability analyses, we also identified key compounds with high druggability likelihood and high binding affinity to KRAS G12D to be recommended for future organic synthesis.
Synthesis of Benfotiamine Prodrug Derivatives and Their Diabetic Neuropathy Activity in C. Elegans Models
Diabetic neuropathy is a type of nerve damage, experienced most commonly through pain and numbness in the legs, that affects more than 200,000 diabetic patients in the US alone. This condition occurs by the following process: when free reducing sugars combine with amino groups or lipids, they can lead to the formation of advanced-glycation end products (AGEs). When AGEs build up, they cause a loss of protein function, impair tissue elasticity, and exaggerate oxidative stress. This process, called glycation, is accelerated in the presence of hyperglycemia, thus contributing to pathogenesis in diabetes. Benfotiamine (BFT) is a synthetic (S-acyl) version of vitamin B1; the natural version, thiamine, can be obtained from whole grains, and deficiency is linked to diabetes. Benfotiamine turns into thiamine in the body and can supplement thiamine. It is a prodrug, a biologically inactive compound that can metabolize into an active form in the body. BFT can clear AGE buildup, by redirecting AGE precursors to the pentose-phosphate pathway instead of the glycation path, and enhancing transketolase, the catalyst for this pathway. Although benfotiamine has been cited as clearing AGE buildup in the body, thereby contributing to managing the symptoms of diabetic neuropathy, BFT has a poor bioavailability. Bioavailability is a measurement of drug absorption, specifically the proportion of a drug that enters circulation, and thus can actually have an effect on the body. BFT’s low absorbance is partially due to its insolubility in oils, so it cannot cross cell membranes unless it is dephosphorylated; as well as its insolubility in water, which is abundant in blood and in cells. Thus, in studies where benfotiamine lessened the pain of diabetic neuropathy, improvement was best with high doses, but this can be dangerous. Therefore, the purpose of this research is to synthesize prodrug derivatives of benfotiamine to increase its bioavailability.
Ethan Fung, Simi Golani, Jenny Lam, Nambita Sahai, Maaya Selvarajan, Rohit Suresh
Synthesis of Neuro-active Rivastigmine and its Effects on Schizophrenia in C. Elegans
Neurodegenerative diseases such as Alzheimer’s and schizophrenia continue to perplex scientists due to their complexity. Our group aims to not only synthesize neuro-active drugs but also test them with various biological assays and observe our results quantitatively in an effort to address the question of the century: Can Neurodegenerative diseases actually be cured?
Shreya Anand, Shloka Raghavan, Udbhav Avadhani, Neha Mandava, Tvisha Nepani, Aishi Rao, Aashi Shah, Alivia Zhang, Audrey Ku, HeeJee Yoon, Elena Green
The Design and Screening of Palmatine Derivatives as G-quadruplex Binding Agents
In this study, we primarily focus on ligands based on the Palmatine scaffold. Palmatine is a protoberberine alkaloid with anticancer properties and relatively high binding affinities to G-quadruplexes (GQUAD). Over a hundred Palmatine-based ligands were created and docked to GQUAD to determine their binding affinities, and an analysis was conducted on them to find the characteristics of molecules that bind well to the complex. The molecules with the highest binding affinities in our library were saved for reference.
Colin Zhang, Felicity Zhou, Rohan Reddy
The design of FTO inhibitors through computational modeling.
The FTO protein is linked with an increased risk of obesity, diabetes, and other cardiovascular diseases. With the increasing rates of obesity and diabetes it is vital to try to combat them. The FTO protein is also one of the biggest influence of polygenic obesity and has the biggest influence on body mass index than all other known genes. Additionally the protein is the first known RNA demethylase and obese people often have higher rates of RNA demethylation. Using computational tools such as autodock, many compounds were designed, tested, and analyzed as potential FTO inhibitors that can inhibit the RNA demethylation caused by the FTO protein.
Nirvan Monangi, Rhea Master, Victoria Salazar, Shivani Ravindra
Total Synthesis of Psychrophillin F and Sansalvamide A
Synthesis, Computation, and Optimization: A Study of the Cyclic Peptide Natural Products Sansalvamide A and Psychrophilin F