Scripps Research Institute

TECHNOLOGY TO EMPOWER CHANGES IN HEALTH (TECH) NETWORK PARTICIPANT TECHNOLOGIES CENTER

CONSORTIUM FOR HIV/AIDS VACCINE DEVELOPMENT

CENTER FOR HIV/AIDS VACCINE IMMUNOLOGY AND IMMUNOGEN DISCOVERY

THE COMPREHENSIVE CENTER FOR CHEMICAL PROBE DISCOVERY AND OPTIMIZATION AT SCRIPPS

CENTER FOR ANTIVIRAL MEDICINES & PANDEMIC PREPAREDNESS (CAMPP) - SUMMARY THE ONGOING COVID-19 PANDEMIC HAS BROUGHT TO LIGHT AN URGENT NEED TO ENHANCE THE THERAPEUTIC PREPAREDNESS FOR FUTURE VIRAL OUTBREAKS AND PANDEMICS. THE OVERARCHING GOAL OF THE “CENTER FOR ANTIVIRAL MEDICINES & PANDEMIC PREPAREDNESS” (CAMPP) IS THUS TO DEVELOP NOVEL STRATEGIES AND ENHANCE THE DRUG DISCOVERY PIPELINES FOR DIRECT-ACTING ANTIVIRALS AGAINST RNA VIRUSES OF PANDEMIC CONCERN. THE SPECIFIC FOCUS OF CAMPP WILL BE TO DEVELOP ANTIVIRALS AGAINST CORONAVIRUSES SARS-COV-2 (SCV2), SARS AND MERS; FLAVIVIRUSES INCLUDING ZIKA, WEST NILE AND DENGUE VIRUS; AND HEMORRHAGIC FEVER VIRUSES INCLUDING THE FILOVIRUS EBOLA, AND BUNYAVIRUSES SEVERE FEVER WITH THROMBOCYTOPENIA SYNDROME VIRUS AND LASSA VIRUS. INFECTION BY ANY OF THESE AGENTS HAS THE POTENTIAL TO CAUSE SEVERE HUMAN DISEASE WITH SIGNIFICANT MORTALITY RATES AND CURRENT OPTIONS FOR ANTIVIRAL TREATMENTS ARE LIMITED. THE ANTIVIRAL DRUG REMDESIVIR AND SEVERAL MONOCLONAL ANTIBODY TREATMENTS HAVE RECEIVED EMERGENCY USE AUTHORIZATION (EUA) FOR TREATMENT OF COVID-19, AND THE POLYMERASE INHIBITOR MOLNUPIRAVIR BY MERCK IS EXPECTED TO BE GRANTED EUA IN THE NEAR FUTURE. MONOCLONAL ANTIBODIES ARE ALSO AVAILABLE TO TREAT EBOLA VIRUS INFECTION, HOWEVER, NONE OF THESE DRUGS CAN BE ADMINISTERED ORALLY, POSING ADDITIONAL CHALLENGES IN TREATING EARLY INFECTION. THERE ARE NO APPROVED TREATMENTS FOR THE CAMPP FLAVIVIRUSES AND HEMORRHAGIC FEVER VIRUSES. TOWARD THIS END, WE HAVE ASSEMBLED A WORLD CLASS MULTIDISCIPLINARY TEAM OF INVESTIGATORS WITH EXPERTISE IN VIROLOGY OF RELEVANT VIRUSES, STRUCTURAL AND COMPUTATIONAL BIOLOGY, CHEMOPROTEOMICS, PHARMACOLOGY AND ORGANOID/ANIMAL MODELS, WHO WILL WORK CLOSELY WITH THE DRUG DEVELOPMENT EXPERTS AT THE DRUG DISCOVERY DIVISION OF THE SCRIPPS RESEARCH INSTITUTE, CALIBR, TO FURTHER THE DEVELOPMENT OF FOUR MAJOR CLASSES OF PROMISING ASSETS IN OUR DRUG DISCOVERY PIPELINE. FIRST, WE PROPOSE TO DEVELOP A POTENTIALLY BEST-IN-CLASS, ORALLY BIOAVAILABLE CORONAVIRUS PROTEASE (CLPRO) INHIBITOR FOR CORONAVIRUSES INCLUDING SCV2, FROM A LATE-STAGE DRUG ASSET UNDERGOING ADME OPTIMIZATION THAT IS EXPECTED TO ENTER IND-ENABLING STUDIES WITHIN THE NEXT THREE YEARS. SECOND, WE WILL IDENTIFY AND OPTIMIZE RNA POLYMERASE INHIBITORS FOR SCV2 AND OTHER CAMPP VIRUSES, WITH THE GOAL OF REACHING IND-ENABLING STUDIES WITHIN THE NEXT FOUR YEARS. THE THIRD FOCUS OF OUR PROPOSAL IS TO DEVELOP ANTIVIRALS AGAINST OTHER ‘DRUGGABLE’ PROTEINS ENCODED BY SCV2 AND ADDITIONAL VIRUSES POSING A PANDEMIC THREAT; THESE ASSETS INCLUDE INHIBITORS OF SCV2 HELICASE, E-PROTEIN ENCODED ION CHANNEL ACTIVITY, ENTRY AND FUSION ACTIVITIES, AND NUCLEOCAPSID, WITH THE GOAL OF OBTAINING IN VIVO PROOF-OF-CONCEPT FOR A SUBSET OF THESE MID-STAGE ASSETS. FINALLY, WE PROPOSE TO TARGET TRADITIONALLY CONSIDERED ‘UNDRUGGABLE’ NON-ENZYMATIC PROTEINS INCLUDING SCV2 AND FLAVIVIRAL STRUCTURAL PROTEINS AS WELL AS RNA STRUCTURE, TO DEVELOP NOVEL STRATEGIES FOR ANTIVIRAL DRUG DEVELOPMENT. CAMPP PROVIDES A HIGHLY INTEGRATED INFRASTRUCTURE OF INVESTIGATORS, EXPERTISE AND EXTERNAL PHARMACEUTICAL AND FOUNDING PARTNERS THAT WILL ENSURE THE CENTER’S SUCCESS IN ACHIEVING OUR GOALS AND NAVIGATING CHALLENGES OF THE DRUG DISCOVERY PROCESS.

SYSTEMS APPROACH TO IMMUNITY AND INFLAMMATION

JOINT CENTER FOR STRUCTURAL GENOMICS

CNS EFFECTS OF ALCOHOL: CELLULAR NEUROBIOLOGY

REVERSING IMMUNE DYSFUNCTION FOR HIV-1 ERADICATION - PROJECT SUMMARY ALTHOUGH THE RATE OF NEW HIV INFECTIONS HAS DECREASED, CONTAINMENT AND EVENTUAL ERADICATION OF THE HIV PANDEMIC REMAINS A TOP PRIORITY IN CONTEMPORARY BIOMEDICAL RESEARCH. ONE OF THE MAJOR CHALLENGES TO HIV CURE IS THE NEED TO RESTORE NORMAL IMMUNE FUNCTION IN ORDER TO EFFECTIVELY ELIMINATE THE ESTABLISHED VIRAL RESERVOIR. WE HAVE ASSEMBLED IN RID-HIV: “REVERSING IMMUNE DYSFUNCTION FOR HIV-1 ERADICATION”, BASIC AND CLINICAL SCIENTISTS WITH EXPERTISE IN VIROLOGY, IMMUNOLOGY, MICROBIOME BIOLOGY, EPIGENETICS, AND SYSTEMS BIOLOGY. IN ADDITION, MERCK RESEARCH LABORATORIES WILL INVEST SIGNIFICANT INTELLECTUAL, HUMAN AND MATERIAL RESOURCES TO COMPLEMENT THE EFFORTS OF THE ACADEMIC SCIENTISTS. THE RID-HIV COLLABORATORY WILL COLLECTIVELY FUNCTION TO EXPLORE THE UNDERLYING BASIS OF THE IMMUNE DYSREGULATION IN HIV-INFECTED INDIVIDUALS AND THE IMPACT IT HAS ON RESERVOIR PERSISTENCE AND VIRAL REBOUND CONTROL. WE WILL TEST FOR THE FIRST TIME SEVERAL INNOVATIVE CONCEPTS, INCLUDING IDENTIFYING EPIGENETIC MECHANISMS IMPRINTED BY THE MICROBIOME AND HOST AND BACTERIAL METABOLOMES THAT PREVENTS THE DEVELOPMENT OF EFFECTIVE INNATE AND ADAPTIVE IMMUNE RESPONSES THAT CAN CONTROL THE SIZE, QUALITY AND ANATOMICAL LOCALIZATION OF THE HIV RESERVOIR. THE OVERARCHING GOAL OF THE RID-HIV COLLABORATORY IS TO PROVIDE PRECLINICAL IN VIVO PROOF-OF- CONCEPT FOR A THERAPEUTIC PARADIGM THAT ENCOMPASSES IMMUNE RESTORATIVE TREATMENTS, USED IN CONCERT WITH ENHANCED VIRAL REACTIVATION AND ELIMINATION STRATEGIES, IN ORDER TO DELIVER A HIV-1 CURE. WE PROPOSE THREE HIGHLY INTEGRATED AND COMPLEMENTARY SCIENTIFIC RESEARCH FOCI (RFS), TO BE SUPPORTED BY RIGOROUS AND ITERATIVE MODELING OF OUTCOMES AND SHAPED BY OUR OUTREACH TO THE HIV COMMUNITY. IN RF1 WE WILL INVESTIGATE THE MECHANISMS WHEREBY HOST- AND MICROBIOME-DERIVED METABOLITES IMPACT INNATE IMMUNE RESPONSES AND INFLUENCE THE MAINTENANCE OF THE LATENT VIRAL RESERVOIR. IN RF2 WE WILL PURSUE THE HYPOTHESIS THAT IN ART/ATI CLINICAL COHORTS, METABOLITES THAT GOVERN INNATE IMMUNITY SHAPE THE ADAPTIVE IMMUNE RESPONSES THAT COULD PREVENT VIRAL REBOUND UPON TREATMENT INTERRUPTION. IN ADDITION, WE WILL EVALUATE THE CAPACITY OF ENGINEERED ALLOGENIC STEM MEMORY T CELLS TO PROVIDE SUPERIOR COGNATE HELP TO PROMOTE THE EFFECTOR FUNCTIONS OF ANTIVIRAL CD8 T CELLS, AND WILL ASSESS THE ABILITY OF FDA-APPROVED AND NOVEL IMMUNE MODULATORS TO RESET THIS BASELINE IMMUNE DYSFUNCTION AND ENHANCE THE FUNCTION OF THIS NOVEL CELL THERAPY PRODUCT. IN RF 3 WE WILL OPTIMIZE A BEST-IN-CLASS LATENCY REVERSAL AGENT (LRA) AND IDENTIFY CLINICAL-STAGE MOLECULES WITH SYNERGISTIC LRA ACTIVITY. CLEARANCE OF REACTIVATED CELLS WILL BE ENHANCED USING A NOVEL STRATEGY FOR NK CELL RECRUITMENT AND BY GENETICALLY MODIFYING B CELLS TO PRODUCE BROADLY NEUTRALIZING HIV-1 ANTIBODIES THAT ENHANCE RESERVOIR CLEARANCE. FINALLY, GENE EDITING WILL BE DEPLOYED FOR IN VIVO TARGETING AND ELIMINATION OF LATENT PROVIRUS NOT AMENABLE TO LRAS. THE OUTCOMES OF STUDIES IN RF1, RF2 AND RF3 WILL ENABLE THE SYNTHESIS OF A PREDICTIVE MATHEMATICAL MODEL TO ESTABLISH THE MOST LIKELY COMBINATIONS OF THERAPIES TO ACHIEVE AN HIV-1 CURE, AND WHICH WILL BE TESTED IN A CAPSTONE AIM TO ESTABLISH PROOF-OF-CONCEPT FOR THESE STRATEGIES IN NHP MODELS AND TO ENABLE TRANSLATION TO THE CLINIC.

CONSORTIUM FOR IMMUNOTHERAPEUTICS AGAINST VIRAL HEMORRHAGIC FEVERS

CONSORTIUM FOR VIRAL SYSTEMS BIOLOGY (CVISB)

SCRIPPS TRANSLATIONAL SCIENCE INSTITUTE

SCRIPPS CLINICAL AND TRANSLATIONAL SCIENCE HUB - PROJECT SUMMARY / ABSTRACT THE SCRIPPS RESEARCH TRANSLATIONAL INSTITUTE (SRTI) IS THE FOUNDATION FOR THE SCRIPPS HUB AND IS DEDICATED TO ACCELERATING SCIENCE THAT WILL IMPROVE HUMAN HEALTH. SRTI’S EMPHASIS ON GENOMICS, DIGITAL MEDICINE, AND INFORMATICS/ANALYTICS FOSTERS A MULTI-DIMENSIONAL UNDERSTANDING OF INDIVIDUALIZED HUMAN HEALTH. THE SCRIPPS HUB HAS PREVIOUSLY INCLUDED THE SCRIPPS RESEARCH INSTITUTE (SR) AND SCRIPPS HEALTH (SH) AS PRINCIPAL PARTNERS, INCLUDING RADY CHILDREN’S INSTITUTE OF GENOMIC MEDICINE (RCIGM) FOR GENOMIC MEDICINE INITIATIVES AND CALIFORNIA INSTITUTE FOR MEDICAL RESEARCH (CALIBR) FOR DRUG REPURPOSING / DISCOVERY. IN THE NEW CTSA CYCLE, OUR PARTNERS HAVE EXPANDED TO INCLUDE SAN DIEGO STATE UNIVERSITY (SDSU), ENABLING US TO COMBINE FORCES IN COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE, BIOSENSORS, AND DIVERSITY INCLUSION AND EQUITY INITATIVES. SRTI’S EXPERTISE IN GENOMICS WAS HIGHLIGHTED DURING THE PANDEMIC. WE BECAME ONE OF THE COUNTRY’S MOST PRODUCTIVE SEQUENCING CENTERS FOR SARS-COV-2 BY RAPIDLY FORMING THE “SEARCH” ALLIANCE TO PROCESS SAMPLES WITH THE SAN DIEGO COUNTY DEPARTMENT OF HEALTH, UCSD, SHARP HEALTH, CALIFORNIA DEPARTMENT OF PUBLIC HEALTH, HELIX, AND OUR PARTNERS RCIGM AND SH. DIGITAL MEDICINE HAS BEEN ONE OF SRTI’S CORE STRENGTHS, HAVING PIONEERED THE FIRST REMOTE, SITE-LESS DIGITAL CLINICAL TRIAL AND NOW EXPANDING THIS METHODOLOGY TO ADDRESS MANY OTHER MEDICAL CONDITIONS SUCH AS HEALTH DURING PREGNANCY AND SLEEP DISORDERS. OUR DIGITAL TRIALS CENTER LAUNCHED THE DIGITAL ENGAGEMENT & TRACKING FOR EARLY CONTROL AND TREATMENT SCRIPPS (DETECT) STUDY, AND IN A MATTER OF WEEKS OUR TEAM WAS ABLE TO ACCURATELY PREDICT THE LIKELIHOOD OF COVID WITH SARS-COV-2 USING PASSIVELY COLLECTED RESTING HEART RATE DATA FROM WRISTBAND SENSORS AND LATER TO IDENTIFY A PHYSIOLOGIC SIGNATURE THAT CORRELATES WITH LONG COVID (POST-ACUTE SEQUELAE OR SARS-COV-2 INFECTION). THE SCRIPPS HUB WILL INNOVATE CLINICAL AND TRANSLATIONAL SCIENCE TO IMPROVE HUMAN HEALTH ACROSS THE LIFESPAN AND DIVERSE RACIAL, ETHNIC, GEOGRAPHIC AND SOCIOECONOMIC COMMUNITIES. THE HUB WILL PROVIDE A NURTURING ENVIRONMENT FOR EDUCATION, TRAINING, AND CAREER DEVELOPMENT WITH A FOCUS ON INDIVIDUALIZED HEALTH DOMAINS OF GENOMICS, DIGITAL MEDICINE, AND BIOMEDICAL INFORMATICS, TO EMPOWER TOMORROW’S DIVERSE WORKFORCE.

PROTEIN CARBOHYDRATE INTERACTIONS IN CELL COMMUNICATION

SCRIPPS TRANSLATIONAL SCIENCE INSTITUTE

JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG-2)

HIV MACROMOLECULAR INTERACTIONS AND IMPACT ON VIRAL EVOLUTION OF DRUG RESISTANCE

ELICITING NEUTRALIZING ANTIBODIES AND B CELL RESPONSES USING NOVEL HIV ENV IMMUNOGENS IN NON-HUMAN PRIMATES - NEUTRALIZING ANTIBODIES ARE LIKELY TO BE REQUIRED FOR AN EFFECTIVE HIV-1 VACCINE. HOWEVER, FEW CANDIDATE VACCINES EFFICIENTLY ELICIT BROADLY NEUTRALIZING ANTIBODIES (BNABS) FOLLOWING VACCINATION. RECENTLY, THE VRC WORKING GROUP HAS ELICITED FUSION PEPTIDE-DIRECTED BNABS IN GUINEA PIGS AND NON-HUMAN PRIMATES (NHPS). SIMILARLY, WE RECENTLY ELICITED BNABS IN RABBITS FOLLOWING HETEROLOGOUS NFL (UNCLEAVED) TRIMER-LIPOSOME PRIME:BOOSTING AT SCRIPPS WHERE WE ACTIVATED B CELL RESPONSES WITH TARGETED N-GLYCAN DELETIONS IN THE PRIMING IMMUNIZATIONS (DUBROVSKAYA ET AL, IMMUNITY 2019). WE ISOLATED TWO RABBIT BNABS THAT RECAPITULATE THE SERUM ACTIVITY. THESE BNABS ARE DIRECTED AGAINST TWO DISTINCT SITES OF ENV VULNERABILITY. THE ELICITATION OF NEUTRALIZING RESPONSES WAS ENHANCED BY TARGETED N-GLYCAN DELETION, HIGH-DENSITY LIPOSOMAL ARRAY AND HETEROLOGOUS TRIMER RESTORATIVE BOOSTING ENV. IN INDEPENDENT EXPERIMENTS IN GUINEA PIGS, WE HAVE ELICITED BNABS IN MULTIPLE ANIMALS ALSO USING A N-GLYCAN DELETION, HETEROLOGOUS ENV NFL PRIME:BOOST APPROACH. THESE RECENT OUTCOMES ARE ENCOURAGING INROADS TOWARD THE SUCCESSFUL SOLUTION OF A 3-DECADE-LONG PROBLEM. THE NEW ERA OF NEAR-NATIVE TRIMERIC SPIKE MIMICS, COUPLED WITH PARTICULATE ARRAY, STRUCTURE-INFORMED DESIGN AND HIGH-RESOLUTION ANALYSIS OF ENV-SPECIFIC B CELL AND LYMPH NODE RESPONSES, AFFORD NEW OPPORTUNITIES TO MORE EFFICIENTLY ELICIT BNABS. WE PROPOSE AN INTEGRATED, MULTI-FACETED APPROACH BLENDING THE EXPERTISE OF WORLD LEADERS IN HIV ENV TRIMER DESIGN, ANALYSIS OF B CELL RESPONSES AND ABS FOLLOWING VACCINATION, NHP IMMUNE TISSUE ANALYSIS AND EM-BASED ANALYSIS OF ONGOING IMMUNE RESPONSES AND HIGH-RESOLUTION AB:TRIMER INTERACTIONS. WE WILL USE WELL-ORDERED TRIMER PRIME:BOOSTING THAT ELICITED BNABS IN RABBITS AND GUINEA PIGS TO ELICIT SUCH RESPONSES IN NHPS, TRANSLATING SUCCESS IN SMALL ANIMALS TO NHPS USING NOVEL IMMUNOGEN DESIGN AND PRESENTATION IN PROJECT 1 (WYATT) AND IMMUNIZATION OF NFL TRIMERS INTO NHPS VIA CORE B (SILVESTRI). WE WILL USE “REAL-TIME” SERUM FAB-TO-TRIMER BINDING EVALUATED BY EM POLYCLONAL IGG EPITOPE MAPPING (EMPEM) IN CORE C (WARD) IN COMPLEMENT WITH RAPID MAB NGS-BASED MAB CLONING, SEQUENCING AND FUNCTIONAL EXPRESSION IN PROJECT 2 (KARLSSON HEDESTAM). IN COLLABORATION WITH THE VRC (MASCOLA) WE WILL DEFINE EITHER NON-NEUTRALIZING MABS TO MASK UNWANTED NON-NEUTRALIZING EPITOPES OR TO BETTER DISPLAY THE EPITOPES OF CROSS-NEUTRALIZING MABS. WE WILL COMPARE NFL TRIMER-LIPOSOMES TO CELL SURFACE NFL TRIMER ARRAY EXPRESSED FROM THE EXCITING MRNA LIPID ENCAPSULATION TECHNOLOGY. WE WILL ASSESS IF IMMUNIZATION IN THE JUVENILE NHP B CELL REPERTOIRE COMPARED TO ADULT MACAQUES WILL BETTER GENERATE BNABS AS IS OBSERVED DURING HUMAN INFECTION. TO FOLLOW OUR DISCOVERY OF A TIER 2 CD4BS-DIRECTED BNAB FOLLOWING TRIMER-LIPOSOME VACCINATION, TERMED E70, WE WILL TARGET THE CD4BS BY DIRECTED NFL TRIMER DEGLYCOSYLATION IN THE NHPS. BASED ON OUR RECENT DISCOVERY OF THE VERY BROADLY NEUTRALIZING VACCINE-INDUCED MAB, 1C2, WE WILL ALSO FOCUS ON THE GP41:120 TRIMER INTERFACE. LEVERAGING THESE INITIAL LEADS, WE WILL UNDERTAKE A MULTIFACETED, CROSS-COMPONENT INTEGRATED APPROACH TO GUIDE THE ELICITATION OF BNABS IN NHPS FOLLOWING VACCINATION WITH NEAR-NATIVE, UNCLEAVED NFL ENV TRIMERS.

GENOMICS FOR KIDNEY TRANSPLANTATION

SCRIPPS TRANSLATIONAL SCIENCE INSTITUTE (UL1)

JCSG CENTER FOR INNOVATIVE MEMBRANE PROTEIN TECHNOLOGIES

HIGH RESOLUTION ANALYSIS OF ENV-DIRECTED B CELLS TO ACCELERATE VACCINE DESIGN

ADULT STEM CELLS FOR THERAPY OF VISUAL DISORDERS

STUDIES OF JOINT AGING AND OSTEOARTHRITIS

NEUTROPHIL LINEAGE IN INFLAMMATION - ABSTRACT NEUTROPHILS CONSTITUTE THE FIRST LINE OF CELLULAR DEFENSE AGAINST PATHOGENIC MICROORGANISMS. IN RESPONSE TO PRO- INFLAMMATORY CUES, UNRESTRICTED NEUTROPHIL ACTIVATION INDUCES TISSUE DAMAGE. TO AVOID DELETERIOUS EFFECTS TO THE HOST, NEUTROPHIL NUMBERS, ACTIVATION, AND LIFESPAN MUST BE TIGHTLY REGULATED, BUT THE MOLECULAR MECHANISMS THAT CONTROL NEUTROPHILS IN THE CONTEXT OF INFLAMMATORY DISEASE REMAIN ELUSIVE. CARDIOVASCULAR DISEASE IS THE LEADING GLOBAL CAUSE OF DEATH. RECENT EVIDENCE SUPPORTS AN IMPORTANT ROLE FOR NEUTROPHILS IN THE DEVELOPMENT OF CORONARY ARTERY DISEASE (CAD). NEUTROPHILS ARE PRESENT IN EARLY AORTIC LESIONS AND IN RUPTURE-PRONE ATHEROSCLEROTIC PLAQUES, AND A POSITIVE CORRELATION BETWEEN PLASMA LEVELS OF NEUTROPHIL SECRETORY PROTEINS AND CAD HAS BEEN ESTABLISHED, SUGGESTING THAT NEUTROPHIL EXOCYTOSIS MEDIATES DETRIMENTAL EFFECTS IN CAD. FURTHERMORE, NEUTROPHIL PRODUCTION IS INCREASED IN THE BONE MARROW IN ATHEROSCLEROTIC MODELS AND NEWLY IDENTIFIED NEUTROPHIL PRECURSORS ARE NOW KNOWN TO MEDIATE INFLAMMATION. HOW NEUTROPHIL SUBSETS CONTRIBUTE TO DISEASE PROGRESSION IN CAD HAS NOT BEEN STUDIED AND THE REGULATION OF NEUTROPHIL DIVERSITY IN DISEASE IS UNKNOWN. THE INFLAMMASOME IS AN EMERGING DRIVER IN ATHEROSCLEROSIS; HOWEVER, THE ROLE OF THE NLRP3 INFLAMMASOME ACTIVATION SELECTIVELY IN NEUTROPHILS ON ATHEROGENESIS HAS NOT BEEN STUDIED AND THE MECHANISMS REGULATING THE FUNCTIONS OF NEUTROPHIL LINEAGE CELLS IN THE CONTEXT OF INFLAMMASOME ACTIVATION AND ATHEROGENESIS REMAIN UNKNOWN. IN THIS SYNERGISTIC PROGRAM, PROJECT 1 NEUTROPHIL DEVELOPMENT DURING INFLAMMATION AND ATHEROSCLEROSIS WILL STUDY HOW NEUTROPHIL HETEROGENEITY IS MODULATED IN HUMAN SUBJECTS WITH CAD, AND HOW THE NLRP3 INFLAMMASOME IN NEUTROPHIL PROGENITORS INFLUENCES GRANULOPOIESIS AND NEUTROPHIL HETEROGENEITY IN ATHEROSCLEROSIS. PROJECT 2 NEUTROPHIL MECHANISMS DURING INFLAMMATION AND ATHEROSCLEROSIS WILL TEST THE HYPOTHESIS THAT HYPERLIPIDEMIA DIFFERENTIALLY REGULATES VESICULAR TRAFFICKING AND ASSOCIATED FUNCTIONS OF NEUTROPHIL PRECURSORS IN CAD, ESTABLISH MECHANISMS OF NLRP3-INDUCED NEUTROPHIL EXOCYTOSIS DYSREGULATION AND IMPLEMENT TRANSLATIONAL APPROACHES TO DECREASE NEUTROPHIL INFLAMMATION IN CAD. PROJECT 3 NEUTROPHIL SURVIVAL AND DEMISE DURING INFLAMMATORY STATES WILL CHARACTERIZE THE EXPRESSION AND FUNCTION OF COMPONENTS OF THE NLRP3 INFLAMMASOME IN CELLS OF THE NEUTROPHIL LINEAGE, AND WILL DEFINE THE EFFECTS OF HYPERLIPIDEMIA-INDUCED INFLAMMATION AND THE ROLES OF DEATH RECEPTOR SIGNALING IN IL-1SS PRODUCTION, MITOCHONDRIAL APOPTOSIS IN VIABILITY OF NEUTROPHIL LINEAGE CELLS, AND NECROPTOSIS SIGNALING IN ATHEROGENESIS. OUR SYNERGISTIC AND UNIQUE PROGRAM USES THE COMPLEMENTARY EXPERTISE OF THREE RENOWN RESEARCHERS, EXPERTS IN THE AREAS OF NEUTROPHIL DEVELOPMENT, NEUTROPHIL INTRACELLULAR FUNCTION REGULATION AND INFLAMMATION, TO STUDY THE CENTRAL HYPOTHESIS THAT UNRESTRICTED ACTIVATION OF NEUTROPHIL PROGENITORS AND MATURE NEUTROPHILS IS A FUNDAMENTAL PROCESS IN CARDIOVASCULAR DISEASE. THESE STUDIES WILL LEAD TO NOVEL APPROACHES TO TREAT NEUTROPHIL-MEDIATED INFLAMMATION IN CAD.

THROMBUS FORMATION AND ANTITHROMBOTIC INTERVENTION

WEST AFRICAN EMERGING INFECTIOUS DISEASE RESEARCH CENTER (WA-EIDRC)

A GENE THERAPEUTIC APPROACH TO STABLE SUPPRESSION OF HIV-1 REPLICATION

CYTOCHROME P-450 POLYMORPHISM

SCALABLE SYNTHESIS AND NEW BOND DISCONNECTIONS

HIV INTERACTIONS IN VIRAL EVOLUTION

SINGLE-MOLECULE DNA SEQUENCING WITH ENGINEERED NANOPORES

ELECTROPHYSIOLOGY OF ALCOHOL IN EXTENDED AMYGDELA

BROADLY EFFECTIVE HCV VACCINE - PROGRAM SUMMARY THE OVERARCHING GOAL OF THIS P01 PROPOSAL IS TO DEVELOP NOVEL HEPATITIS C VIRUS (HCV) VACCINE CANDIDATES THAT CAN ELICIT POTENT BROADLY NEUTRALIZING ANTIBODY RESPONSES IN IMMUNIZATION. DESPITE HIGHLY EFFECTIVE ANTIVIRAL DRUGS AGAINST HCV NOW BEING AVAILABLE, THE CONTINUOUS INCREASE IN NEW INFECTIONS UNDERSCORES THE REAL-WORLD CHALLENGES IN COMBATING THIS HUMAN INFECTION WITHOUT A VACCINE. THIS P01 PROPOSAL “BROADLY EFFECTIVE HEPATITIS C VACCINE” IS BUILT ON THE HYPOTHESIS THAT AN HCV VACCINE EFFECTIVE AGAINST DIVERSE CIRCULATING HCV STRAINS CAN BE DEVELOPED THROUGH RATIONAL ENGINEERING OF VACCINES TO ENHANCE ANTIGEN IMMUNOGENICITY AND PRESENTATION OF CONSERVED NEUTRALIZING EPITOPES, AND TO TARGET WELL-DEFINED MULTIDONOR CLASS BROADLY NEUTRALIZING ANTIBODY (BNAB) RESPONSES TO HCV. MULTIDONOR CLASS ANTIBODY RESPONSES ARE ANTIBODIES SHARING COMMON GENETIC AND FUNCTIONAL FEATURES PRODUCED IN INFECTION OR VACCINATION AT THE POPULATION LEVEL. THIS P01 PROGRAM CONSISTS OF 2 RESEARCH PROJECTS, SUPPORTED BY AN ADMIN CORE AND 2 SCIENTIFIC CORES. THE OVERALL AIMS OF THE PROGRAM ARE: (1) TO DETERMINE THE STRUCTURES OF HCV ENVELOPE GLYCOPROTEINS IMPORTANT FOR RATIONAL VACCINE DESIGN; (2) TO RATIONALLY DESIGN HCV VACCINE ANTIGENS FOR ELICITATION OF BROADLY NEUTRALIZING ANTIBODIES THAT WILL BE EFFECTIVE AGAINST DIVERSE CIRCULATING VIRAL STRAINS; (3) TO DETERMINE THE ANTIBODY RESPONSES ELICITED BY HCV VACCINE ANTIGENS IN PRECLINICAL ANIMAL MODELS. SUCCESS IN THIS RESEARCH PROGRAM WILL RESULT IN BOTH BASIC SCIENTIFIC KNOWLEDGE AND A STRONG HCV VACCINE CANDIDATE FOR FUTURE PILOT PRODUCTION AND CLINICAL TESTING.

NEURPSYCHOPHARMACOLOGY-MULTIDISCIPLINARY TRAINING

FOUR-DIMENSIONAL HETEROGENEITY OF FLUID PHASE BIOPSIES IN CANCER (4DB-CENTER)

MOLECULAR MECHANISMS LINKING AGING, ABETA PROTEOTOXICITY AND NEURODEGENERATION

DEVELOPMENT AND ADVANCEMENT OF BROAD-SPECTRUM RESPIRATORY ANTIVIRALS

MICRORNAS FOR THERAPY OF VISUAL DISORDERS

RESISTANCE DRIVEN STRUCTURAL DESIGN FOR HIV THERAPIES

CHEMICAL PROTEOMIC PLATFORMS FOR RADICALLY EXPANDING CANCER DRUGGABILITY

DEVELOPMENT OF CARBOXYL- AND AMIDE-DIRECTED C-H ACTIVATION/C-C COUPLING REACTIONS

ANTIBODY EFFECTOR FUNCTION IN PROTECTION AGAINST HIV-1

AUTODOCK SOFTWARE DEVELOPMENT AND MAINTENANCE

ROLE OF RAB27 IN GRANULOCYTE FUNCTION

INTEGRATIVE NEUROSCIENCE INITIATIVE ON ALCOHOLISM - WEST - SUPPLEMENT

MANAGING ATHEROSCLEROSIS BY MODULATING HDL FUNCTION

DEVELOPMENT OF OREXIN-1 RECEPTOR ANTAGONISTS FOR DRUG ADDICTION

CHEMOPROTEOMIC IDENTIFICATION AND THERAPEUTIC VALIDATION OF PROTEINS OF METABOLIC SIGNIFICANCE

PROTEOMIC ANALYSIS OF PLASMINOGEN RECEPTORS

PROBING THE BIOCHEMICAL MECHANISM OF AMYLOID DISEASE

DISSECTING POLYCLONAL SERA TO REVEAL CORRELATES OF PRODUCTIVE IMMUNE RESPONSES TO HIV

DESIGN AND TESTING OF GERMLINE-TARGETING AND BOOSTING IMMUNOGENS TO ELICIT 10E8-LIKE BROADLY NEUTRALIZING ANTIBODIES AGAINST HIV

MULTIDIMENSIONAL DEVELOPMENT OF HIGH-AFFINITY ANTI-GLYCAN ANTIBODIES TO FIGHT DEADLY BACTERIAL INFECTIONS - ABSTRACT THE DEVELOPMENT OF IMMUNOTHERAPIES FOCUSED ON THE SURFACE GLYCANS OF BACTERIA IS HYPOTHESIZED TO BE A POTENTIAL PARADIGM SHIFT IN THE FIGHT AGAINST LIFE-THREATENING AND ANTIBIOTIC-RESISTANT BACTERIA, AN EMERGING AND INCREASING HEALTH CONCERN FOR WHICH THERAPEUTIC OPTIONS ARE LIMITED. OUR PO1 TEAM WILL USE CHEMISTRY TO DECONSTRUCT AND DISPLAY BACTERIAL GLYCAN STRUCTURES ON AN ARTIFICIAL PLATFORM TO MAKE THEM IMMUNOGENIC AND RECOGNIZED BY THE IMMUNE SYSTEM. IMMUNE RESPONSES WILL BE ANALYZED AND DISSECTED BY BACTERIOLOGISTS, CELLULAR AND STRUCTURAL IMMUNOLOGISTS TO DETERMINE THE CHARACTERISTICS OF WHAT MAKES A VACCINE OR AN ANTIBODY AGAINST GLYCANS EFFECTIVE AS AN ANTIBIOTIC AND DEPLOYABLE IN PRE-CLINICAL STUDIES. THIS PROGRAM THAT ASSEMBLES SOME OF THE WORLD EXPERTS IN THEIR RESPECTIVE FIELDS IS AMBITIOUS AND INTENDS TO PIONEER THE EFFORT OF PLACING IMMUNOTHERAPY NEXT TO CHEMOTHERAPY FOR THE TREATMENT OF BACTERIAL INFECTIONS. OUR UNIQUE COMBINATION OF CHEMISTRY-IMMUNOLOGY- BACTERIOLOGY-STRUCTURAL BIOLOGY WILL PROVIDE THE NECESSARY MECHANISTIC UNDERSTANDING OF WHAT QUALIFIES A VACCINE OR AN ANTIBODY TO BE EFFECTIVE IN IMMUNOTHERAPY. THE TEAM IS ALREADY PRODUCTIVE AND HAS PUBLISHED THE PROOFS OF PRINCIPLE OF THE APPROACH ON WHICH THE SCIENCE OF THIS APPLICATION IS BASED: VERY HIGH AFFINITY ANTIBODIES CAN BE PRODUCED AGAINST BACTERIAL GLYCANS EXPOSED AT THE SURFACE OF ANTIBIOTIC RESISTANT BACTERIA AND ARE EFFECTIVE AT COMBATING INFECTIOUS CHALLENGES. WE WILL EXPAND OUR STRATEGY TO THE SURFACE GLYCANS OF THREE BACTERIAL PATHOGENS LISTED BY WHO AS “CRITICAL” OR “HIGH” PRIORITY: STAPHYLOCOCCUS AUREUS, KLEBSIELLA PNEUMONIAE, AND NEISSERIA GONORRHEA. THE FUNDAMENTAL KNOWLEDGE THAT WE WILL GAIN FROM OUR STUDIES SHOULD ESTABLISH A VERY DETAILED BLUEPRINT OF THE IMMUNE RECOGNITION OF GLYCANS AND GLYCOPEPTIDES BY THE IMMUNE SYSTEM. THE INTEGRATION OF THE CHEMISTRY, IMMUNOLOGY, AND STRUCTURAL BIOLOGY FACETS OF THE PROJECT DIRECTLY INTO THE BACTERIOLOGY AND IN VIVO MODELS, WILL IDENTIFY GLYCANS TARGETS AND STRATEGIES TO INITIATE PRE-CLINICAL STUDIES.

PRECLINIAL DEVELOPMENT OF JNK3 INHIBITORS TO TREAT PARKINSON'S DISEASE

KNOCKIN MICE EXPRESSING BROADLY NEUTRALIZING HIV ANTIBODIES 4E10 AND B12

ELUCIDATING CARDIOVASCULAR PHENOTAYPES EMPLOYING GENOME EDITING OF IPS CELLS

STRUCTURE AND FUNCTION OF PROTEIN C

EPIGENOMIC MODULATION OF CYSTIC FIBROSIS

CANCER GENES: TRANSLATING BASICS TO APPLICATIONS

PROTEOGENETICS

REGULATION OF PROTEIN C PATHWAYS

ANTITUMOR ANTIBIOTICS

THE MULTI-OMICS VACCINE EVALUATION (MOVE) CONSORTIUM - PROJECT SUMMARY AN HIV VACCINE REPRESENTS OUR BEST OPPORTUNITY FOR ELICITING DURABLE, PROTECTIVE IMMUNITY AND ENDING THE DECADES-LONG AIDS PANDEMIC. TO BE SUCCESSFUL, AN ANTIBODY-BASED HIV VACCINE MUST RELIABLY INDUCE BROADLY NEUTRALIZING ANTIBODIES (BNABS), MOST LIKELY VIA A SERIES OF IMMUNOGENS OR MIXTURES OF IMMUNOGENS DELIVERED SEQUENTIALLY. TO AVOID VIRAL ESCAPE, BNABS OF AT LEAST 2-3 DISTINCT SPECIFICITIES MUST BE INDUCED CONCURRENTLY. THUS, A MORE HOLISTIC VIEW OF HIV VACCINE COMPOSITION WOULD RESEMBLE A MATRIX OF IMMUNOGENS RATHER THAN A SEQUENCE. CONSTRUCTING A SINGLE SET OF IMMUNOGENS THAT RELIABLY INDUCE BREADTH AGAINST JUST ONE EPITOPE IS A DAUNTING CHALLENGE. SUCCEEDING IN THE EXPONENTIALLY MORE DIFFICULT TASK OF ASSEMBLING A COHESIVE IMMUNOGEN MATRIX WILL REQUIRE SIGNIFICANT IMPROVEMENTS IN THE SPEED AND GRANULARITY WITH WHICH WE CAN DESIGN AND EVALUATE VACCINES. HERE, WE PROPOSE A SOLUTION: BY EMBEDDING MULTI-OMICS TECHNOLOGY AT EACH STAGE OF IMMUNOGEN DEVELOPMENT, WE CAN UNLOCK A REVOLUTIONARY INCREASE IN SCALE WHILE SIMULTANEOUSLY IMPROVING THE DEPTH AND RESOLUTION OF OUR ANALYSES. THE MULTI-OMICS VACCINE EVALUATION (MOVE) CONSORTIUM BRINGS TOGETHER A MULTI- DISCIPLINARY TEAM OF EXPERT INVESTIGATORS WITH A LONG HISTORY OF PRODUCTIVE COLLABORATION. OUR CENTRAL HYPOTHESIS IS THAT DEEPLY INTEGRATING ADVANCED MULTI-OMICS APPROACHES THROUGHOUT OUR ITERATIVE VACCINE DEVELOPMENT PIPELINE WILL SPEED THE DISCOVERY OF AN HIV VACCINE BY ALLOWING US TO OPERATE CONCURRENTLY ACROSS MULTIPLE IMMUNOGENS. OUR OVERALL MISSION IS TO ACCELERATE DEVELOPMENT OF AN HIV VACCINE BY PARALLELIZING THE DESIGN AND TESTING OF A MATRIX OF COMPLEMENTARY IMMUNOGENS THAT RELIABLY INDUCE BROAD, DURABLE IMMUNITY. TO ACCOMPLISH OUR OBJECTIVES, WE PROPOSE THE FOLLOWING SPECIFIC AIMS: SPECIFIC AIM 1: PROFILE THE HUMAN IMMUNOGENICITY OF A NOVEL V2 APEX-FOCUSING ENV TRIMER. SPECIFIC AIM 2: EVALUATE Q23-ELICITED IMMUNE RESPONSES, CANDIDATE BOOSTING IMMUNOGENS, AND DELIVERY STRATEGIES IN HUMANIZED ANIMAL MODELS. SPECIFIC AIM 3: DEVELOP THE Q23 BACKBONE INTO A MULTI-EPITOPE PRIMING IMMUNOGEN.

UNUSUAL PHARMACOPHORES AND NEW TOOLS FOR CROSS-COUPLING

PLANB2CUREHIV (THE 'PLANB' CONSORTIUM) - PROJECT SUMMARY ANTIBODIES CAPABLE OF NEUTRALIZING THE GLOBAL DIVERSITY OF HIV STRAINS ARE DIFFICULT TO ELICIT IN HUMANS. THIS IS BECAUSE SUCH ANTIBODIES REQUIRE UNUSUAL FEATURES DERIVING FROM RARE PRECURSOR B CELLS THAT MUST UNDERGO EXTENSIVE AFFINITY MATURATION. TO DATE, ONLY A SMALL NUMBER OF POTENT BROADLY NEUTRALIZING ANTIBODIES (BNABS) HAVE BEEN ISOLATED AFTER SCREENING THOUSANDS OF PATIENTS RESPONDING TO UNSUPPRESSED INFECTION. PASSIVE IMMUNIZATION WITH RECOMBINANT MONOCLONAL HIV BNABS HOWEVER, CAN MAINTAIN SUPPRESSION OF VIREMIA IN PATIENTS AFTER ANTI-RETROVIRAL TREATMENT (ART) INTERRUPTION FOR AS LONG AS SERUM TITERS REMAIN ABOVE THRESHOLD EFFECTIVE SERUM CONCENTRATIONS. THIS SUGGESTS THAT ESTABLISHING DURABLE BNAB TITERS ABOVE THESE THRESHOLDS COULD RESULT IN AN HIV FUNCTIONAL CURE, DEFINED AS LIFE-LONG SUPPRESSION OF VIREMIA. SINCE HIV BNABS CANNOT BE ELICITED THROUGH VACCINATION, GENE THERAPIES ARE BEING CONSIDERED AS AN APPROACH TO DELIVER SUCH LONG- LASTING BNAB TITERS IN VIVO. OF THESE, GENOME-EDITED B CELLS ARE A NOVEL AND PROMISING APPROACH THAT MAY HOLD SEVERAL KEY ADVANTAGES. PRIMARY B CELL ANTIGEN RECEPTORS (BCRS) CAN BE REPROGRAMMED TO EXPRESS NOVEL SPECIFICITIES BY INSERTING ANTIBODY TRANSGENE CASSETTES INTO THE IGH-LOCUS DOWNSTREAM OF ENDOGENOUS HEAVY CHAIN (HC) IMMUNOGLOBULIN (IG) VARIABLE REGION EXONS. THESE MODIFIED CELLS CAN BE EXPANDED AND DIFFERENTIATED IN VIVO BY VACCINATION INTO MEMORY AND LONG-LIVED PLASMA CELLS THAT CAN DURABLY SECRETE THE NEW ANTIBODY SPECIFICITY IN WILD TYPE IMMUNOCOMPETENT MICE BY INDEPENDENT RESEARCH GROUPS. THE OVERALL PURPOSE OF THE PLANB CONSORTIUM IS TO ACCELERATE THE PRE-CLINICAL DEVELOPMENT OF SAFE AND EFFECTIVE IGH- REPROGRAMMED B CELL-BASED THERAPIES THAT WOULD PROVIDE LIFE-LONG BNAB TITERS CAPABLE OF MAINTAINING SUPPRESSION OF THE VIRAL RESERVOIR, ALLOWING PATIENTS TO DISCONTINUE ART THERAPY. OUR AIM IS TO DEVELOP AND COMPARE TWO DISTINCT OPTIONS FROM WHICH ONE COULD BE SELECTED FOR CLINICAL DEVELOPMENT UPON COMPLETION OF THE PROGRAM. THE FIRST IS AN EX VIVO REPROGRAMMED B CELL PRODUCT THAT CAN BE AUTOLOGOUSLY TRANSFERRED AND VACCINATED IN PATIENTS. THE SECOND IS AN IN VIVO B CELL TARGETING AND IGH-REPROGRAMMING SYSTEM THAT WILL BE USED IN CONJUNCTION WITH VACCINATION. IN BOTH CASES, DURABLE HIV BROADLY NEUTRALIZING ANTIBODY MEMORY RESPONSES MUST BE ELICITED FROM THE ENGINEERED CELLS.

GERMLINE TARGETING INFLUENZA IMMUNOGENS

ACTIVITY DEPENDENT CONTROL OF VISUAL SYSTEM DEVELOPMENT

FAAH: STRUCTURE, FUNCTION, AND IN VIVO INHIBITION

STUDIES ON MICROTUBULE BINDING PROTEINS

NOVEL PROTEOMICS APPROACH TO HIV-ASSOCIATED NEUROCOGNITIVE DISORDER & DRUG ABUSE

CELL SPECIFIC PERTURBATIONS OF THE PROTEOME IN ALZHEIMER'S DISEASE - ALZHEIMER’S DISEASE (AD) IS THE LEADING CAUSE OF AGING-RELATED COGNITIVE DECLINE, AFFECTING MORE THAN 5 MILLION AMERICANS OVER 65 YEARS OLD, AND THE NUMBER OF PATIENTS IS EXPECTED TO CLIMB TO 13 MILLION AS BABY BOOMERS AGE. OUR ABILITY TO LEARN AND REMEMBER DECLINES WITH AGE DUE TO PROGRESSIVE CHANGES IN SYNAPTIC CONNECTIVITY AND FUNCTION. SYNAPTIC ABNORMALITIES ALSO COMMONLY PRECEDE NEURONAL LOSS DURING EARLY STAGES OF ALZHEIMER’S DISEASE (AD) AND OTHER NEURODEGENERATIVE DISORDERS. HOWEVER, WE ARE ONLY BEGINNING TO UNDERSTAND THE FULL SPECTRUM OF THESE ABNORMALITIES, THEIR CONTRIBUTIONS TO COGNITIVE DECLINE, AND THE UNDERLYING MECHANISMS. THIS CHALLENGE IS LARGELY ATTRIBUTED TO THE COMPLEXITY OF THE BRAIN AND ETIOLOGIES OF AGING AND NEURODEGENERATION. HALLMARKS OF ADVANCED ALZHEIMER’S DISEASE (AD) INCLUDE ACCUMULATIONS OF EXTRACELLULAR AMYLOID PEPTIDES AND INTRACELLULAR HYPERPHOSPHORYLATED TAU PROTEIN AS WELL AS CHRONIC NEUROINFLAMMATION. WHILE GENES FOR FAMILIAL AD HAVE BEEN IDENTIFIED, WHICH SHED SUBSTANTIAL LIGHT ON THE ETIOLOGY OF THE DISEASE, THE MECHANISMS BEHIND SPORADIC ONSET AD STILL REMAIN A MYSTERY. WHILE STUDIES OF TRANSCRIPTIONAL DYNAMICS IN THE BRAIN HAVE BEEN TRANSFORMATIVE, TRANSCRIPTIONAL DYNAMICS DO NOT CORRELATE WELL WITH PROTEIN DYNAMICS BECAUSE PROTEIN SYNTHESIS, TURNOVER AND SUBCELLULAR LOCALIZATION ARE MORE TIGHTLY REGULATED SPATIALLY AND TEMPORALLY THAN TRANSCRIPTION. STUDIES HAVE SUGGESTED THAT PROTEOSTASIS DECLINES WITH AGE, IMPAIRING CELLS FROM MANAGING THE INEVITABLE MISFOLDING OF PROTEINS. OUR TEAM WILL STUDY PROTEIN DYNAMICS IN ANIMAL MODELS BASED ON BIO-ORTHOGONAL NON-CANONICAL AMINO ACID (BONCAT) PROTEIN LABELING. THESE METHODS ALLOW US TO MEASURE DYNAMICS IN PROTEIN SYNTHESIS AND DEGRADATION IN SPECIFIC BRAIN CELL TYPES RELEVANT TO AD. THESE MEASUREMENTS WILL PROVIDE NEW INFORMATION ABOUT THE DISRUPTION OF NORMAL CELLULAR PROCESSES. THE OVERREACHING GOAL OF OUR COLLABORATIVE PROPOSAL IS TO BRIDGE CRITICAL GAPS IN KNOWLEDGE BY LEVERAGING THE STATE-OF-THE-ART METHODS FOR BIO-ORTHOGONAL NON-CANONICAL AMINO ACID TAGGING (BONCAT) AND QUANTITATIVE MASS SPECTROMETRY (MS) TO IDENTIFY BRAIN CELL-TYPE CONTRIBUTIONS TO SYNAPTIC AND NEURONAL DECLINE ASSOCIATED WITH AD.

CFTR PROCESSING IN THE ENDOPLASMIC RETICULUM

BIOLOGICALLY ACTIVE CYCLIC PEPTIDES

NOVEL CHEMICAL AND IMMUNOLOGICAL APPROACHES TO INFLUENZA THERAPY

RISK FACTORS FOR ALCOHOLISM IN NATIVE AMERICANS

IN VIVO INCORPORATION OF UNNATURAL AMINO ACIDS

INTEGRINS AND OCULAR ANGIOGENESIS

GENE NETWORK PERTURBATIONS IN ALCOHOL DEPENDENCE - A SYSTEMS BIOLOGY APPROACH

MECHANISMS OF FORCE SENSING IN THE NERVOUS SYSTEM

STRUCTURE-FUNCTION OF CYTOPROTECTIVE COAGULATION PROTEASES AND THEIR RECEPTORS

NATIONAL RESOURCE FOR AUTOMATED MOLECULAR MICROSCOPY

EEG AND ERP MEASURES OF ALCOHOL'S EFFECTS

DISCOVERING SMALL MOLECULES ACTIVATORS OF STRESS RESPONSIVE SIGNALING

SMALL MOLECULE THERAPEUTICS FOR BOTULLINUM NEUROTOXIN A

THE NOCICEPTIN ORL1 SYSTEM: TREATMENT TARGET FOR RELAPSE

THE ROLE OF CYCLIN E IN GROWTH CONTROL AND TUMOROGENESIS

MEDICATION DEVELOPMENT FOR PROTRACTED ABSTINENCE IN ALCOHOLISM

RESOURCE FOR STRUCTURE-BASED COMPUTATIONAL DRUG DISCOVERY AND DESIGN (RSD3) - PROJECT SUMMARY AUTOMATED DOCKING IS A COMPUTATIONAL METHOD THAT IS NOW ROUTINELY USED FOR IDENTIFYING SMALL MOLECULES THAT HAVE THE POTENTIAL TO BE NEW DRUGS. OVER THE PAST THREE DECADES WE HAVE DEVELOPED DOCKING METHODS AND OUR DOCKING SOFTWARE AUTODOCK IS NOT THE MOST CITED DOCKING SOFTWARE WITH OVER 40,000 CITATIONS IN THE PEER REVIEWED LITERATURE. AS SUCH, IT HAS BECOME AN IMPORTANT RESOURCE FOR THE COMMUNITY. WE SEEK TO CREATE A NATIONAL RESOURCE THAT WILL ALLOW US TO MAINTAIN AND MODERNIZE THIS SOFTWARE TO ADAPT TO EVOLVING HARDWARE PLATFORMS AND OPERATING SYSTEMS, TO KEEP THE SOFTWARE UP TO DATE AND RELEVANT BY INCORPORATING THE LATEST ALGORITHMIC DEVELOPMENTS, AND TO SUPPORT ITS LARGE USER COMMUNITY. IN PARALLEL WITH THESE EFFORTS, AN IMPORTANT GOAL OF THE PROPOSED RESOURCE IS TO CHART A PATH TOWARD A SELF-SUSTAINED SOFTWARE ECOSYSTEM WHERE CONTRIBUTORS FROM AROUND THE WORLD WILL CONTRIBUTE TO MAINTAIN AND FURTHER DEVELOP THIS SOFTWARE AFTER THE LIFETIME OF THIS AWARD. THIS GOAL HAS BEEN ACHIEVED BY OTHER SUCCESSFUL OPEN SOURCE PROJECTS SUCH AS DEBIAN AND PYTHON, AND THE WRITTEN INTEREST OF MANY COLLEAGUES BOLSTER OUR CONFIDENCE THAT THE AUTODOCK SOFTWARE TOO CAN REACH THIS GOAL. TO THIS END WE PROPOSE THREE SPECIFIC AIMS. OUR FIRST AIM IS TO MAINTAIN AND MODERNIZE THE SOFTWARE CODE. THIS CRITICAL WORK IS NEEDED FOR THE SOFTWARE TO REMAIN FUNCTIONAL AND ABLE TO ADDRESS THE EVOLVING NEEDS OF THE COMMUNITY. AS WE OVERHAUL THE SOFTWARE, WE WILL LEVERAGE NEWER TOOLKITS FOR GENERATING MODERN AND INTUITIVE GRAPHICAL USER INTERFACES. THESE INTERFACES ENABLE RESEARCHERS, SUCH AS CLINICAL PHYSICIANS OR CHEMISTS WITH LIMITED COMPUTATIONAL SKILLS FOR INSTANCE, TO USE DOCKING TO BETTER UNDERSTAND THE MECHANISM OF ACTION OF A DRUG AND OPTIMIZE IT. OUR SECOND AIM IS CONCERNED WITH MAKING OUR SOFTWARE TOOLS INTEROPERABLE WITH OTHER IMPORTANT MODELING SOFTWARE TOOLS SUCH AS MOLECULAR DYNAMICS FOR INSTANCE. NOT ONLY DOES THIS AUGMENT THE POTENTIAL OF DOCKING TO LEAD TO NOVEL THERAPEUTIC MOLECULES, BUT IT ALSO SERVES OUR GOAL TO CREATE A COMMUNITY OF DEVELOPERS WHO WILL ULTIMATELY MAINTAIN THIS SOFTWARE ECOSYSTEM. FINALLY OUR THIRD AND FINAL AIM IS ABOUT SUPPORTING THE LARGE USER COMMUNITY, GROWING IT AND ENSURING THAT THE SOFTWARE IS EASILY DISCOVERED, OBTAINED AND INSTALLED. WE HAVE A LONG TRACK RECORD OF DEVELOPING OPEN SOURCE SOFTWARE PROMOTING BEST PRACTICES IN SOFTWARE ENGINEERING, AND MAKING THESE TOOLS USABLE, USEFUL, AND AVAILABLE TO THE COMMUNITY. LIKEWISE WE HAVE SUPPORTED AND GROWN OUR USER COMMUNITY FOR MANY YEARS. THIS PUTS US IN A UNIQUE POSITION TO CREATE THE PROPOSED RESEARCH WHICH, IF FUNDED, WILL ALLOW US TO CONVERT THIS VALUABLE SOFTWARE CODE INTO A COMMUNITY SUPPORTED SOFTWARE ECOSYSTEM ENSURING THAT THIS SOFTWARE WILL CONTINUE TO SUPPORT THE DESIGN OF NOVEL THERAPEUTIC MOLECULES BEYOND THE LIFETIME OF THIS AWARD.

RIBONUCLEOPROTEIN COMPLEXES REGULATING T-CELL ACTIVATION

GENETIC CONTROL OF DEVELOPMENT

BUILDING A SOMATOSENSORY ATLAS FOR INTEROCEPTION - PROJECT SUMMARY/ABSTRACT SOMATOSENSORY NEURONS ARE WELL-KNOWN FOR INNERVATING SKIN AND MUSCLE AND TRANSMITTING SENSATIONS SUCH AS TOUCH, PAIN, ITCH, AND PROPRIOCEPTION TO THE BRAIN. HOWEVER, THESE SAME TYPE OF HETEROGENEOUS SET OF NEURONS ALSO INNERVATE INTERNAL ORGANS AND ARE RESPONSIBLE TO CONVEY INFORMATION OF THE INTERNAL STATE OF OUR BODY. THESE INTEROCEPTIVE SIGNALS INCLUDE BOTH CONSCIOUS (BLADDER FULLNESS) AND SUBCONSCIOUS (BLOOD PRESSURE) SENSES. DESPITE THEIR IMPORTANCE, WE DO NOT KNOW THEIR PROJECTION PATTERNS AND PHYSIOLOGICAL ROLES. HERE, WE PROPOSE TO USE A SET OF INNOVATIVE TOOLS THAT WILL ALLOW US TO SPECIFICALLY LABEL, VISUALIZE, AND ISOLATE SENSORY NEURONS INNERVATING VARIOUS INTERNAL ORGANS. USING A VARIETY OF STATE-OF-ART MOLECULAR, IMAGING, AND GENOMIC TECHNIQUES, WE WILL BUILD AN ANATOMICAL DATABASE OF THESE NEURONS AND USE SNRNASEQ TO ESTABLISH THE MOLECULAR IDENTITIES OF INDIVIDUAL SENSORY NEURONS BASED ON THEIR INNERVATING ORGANS. FINALLY, THE ANATOMICAL, CELLULAR, AND MOLECULAR MAPS WILL BE STANDARDIZED, INDEXED, AND INTEGRATED INTO AN ATLAS THAT WILL ALLOW THE COMMUNITY TO FREELY ACCESS THE DATA.

BIOGPS: EXTENSIBLE WEB 2.0 GENE PORTAL FOR STRUCTURED AND UNSTRUCTURED ANNOTATION

INTEGRATIVE OMICS ANALYSIS OF HUMAN CARTILAGE IN AGING AND OSTEOARTHRITIS

STRUCTURAL AND MECHANISTIC BASIS FOR RNA SILENCING

PROTEIN DYNAMICS IN DIHYDROFOLATE REDUCTASE CATALYSIS

TRANSCRIPTIONAL CONTROL OF SYNAPTIC PLASTICITY BY CLASS IIA HDACS

SINGLE NUCLEUS GENE EXPRESSION IN MODERATE AND COMPULSIVE OPIOID SELF-ADMINISTRATION IN A RODENT MODEL OF HIV - SUMMARY THE ABUSE OF OPIOID DRUGS IS ASSOCIATED WITH TREATMENT NON-COMPLIANCE, GREATER RISK OF VIRAL TRANSMISSION, AND MORE RAPID CLINICAL PROGRESSION OF HIV DISEASE. THE OVERARCHING HYPOTHESIS BEHIND THE PRESENT PROJECT IS THAT THE ANALYSIS OF MOLECULAR PROFILES OF NEURONAL AND GLIA CELLS AT THE SINGLE CELL LEVEL IN DRUG ABUSE-RELEVANT BRAIN REGIONS BY SINGLE NUCLEUS RNA-SEQ (SNRNA-SEQ) WILL REVEAL KEY GENES THAT ARE DYSREGULATED BY THE INTERACTION OF HIV WITH OPIOID ABUSE, RESULTING IN NEURODEGENERATION AND COGNITIVE IMPAIRMENT. TO TEST THE PRESENT HYPOTHESIS, WE PROPOSE TO USE VALIDATED SYSTEMS BIOLOGY STRATEGIES FOR THE RECONSTRUCTION AND INTERROGATION OF A GENOME-SCALE INTEGRATED GENE REGULATORY NETWORK IN CONJUNCTION WITH SNRNA-SEQ FROM HIV TRANSGENIC (TG) RATS, WHICH HARBOR A NON-REPLICATING HIV-1 TRANSGENE EXPRESSING CHRONIC LOW-LEVELS OF MULTIPLE HIV-1 PROTEINS IN DISEASE-RELEVANT CELL TYPES, AND WILD-TYPE RATS. THE OCCASIONAL BUT LIMITED USE OF A DRUG IS CLINICALLY DISTINCT FROM DEPENDENT DRUG USE, WHICH IS CHARACTERIZED BY THE EMERGENCE OF DEPENDENCE AND A NEGATIVE EMOTIONAL STATE WHEN ACCESS TO THE DRUG IS PREVENTED THAT DRIVES NEGATIVE REINFORCEMENT, A POWERFUL SOURCE OF MOTIVATION FOR DRUG SEEKING. THEREFORE, WE WILL USE A STATE-OF-THE-ART PARADIGM OF VOLUNTARY INTRAVENOUS OPIOID SELF-ADMINISTRATION UNDER SHORT ACCESS (SHA) CONDITIONS, WHICH IS CHARACTERIZED BY A NON-DEPENDENT, “RECREATIONAL” PATTERN OF DRUG USE, AND LONG ACCESS (LGA) CONDITIONS, WHICH LEADS TO DEPENDENT DRUG INTAKE. ESCALATED DRUG INTAKE UNDER LGA CONDITIONS IS HIGHLY RELEVANT TO HUMAN SUBSTANCE USE DISORDER (SUD) AS IT HAS BEEN SUGGESTED THAT IT MODELS ALL 7 OF THE CRITERIA FOR DRUG ADDICTION IN THE DIAGNOSTIC AND STATISTICAL MANUAL OF MENTAL DISORDERS (DSM)-IV AND 7 OF THE 11 CRITERIA IN THE DSM-V. WE SHOWED THAT HIV TG RATS SELF-ADMINISTERING OXYCODONE IN THIS LGA PARADIGM OF ESCALATED SELF-ADMINISTRATION DISPLAY INCREASED NEURAL INJURY AND COGNITIVE IMPAIRMENT. THE PROJECT WILL ADDRESS THE FOLLOWING VEXING QUESTION ABOUT OPIOID ABUSE IN THE SETTING OF HIV INFECTION: WHAT ARE THE CELL TYPES AND CELL STATES THAT DRIVE NEUROINFLAMMATION, NEURODEGENERATION, VIRUS EXPRESSION, AND ESCALATED (DEPENDENT) OPIOID SELF-ADMINISTRATION AND COGNITIVE IMPAIRMENT IN THE SETTING OF HIV? OVERALL, THIS COLLABORATIVE INTERDISCIPLINARY PROPOSAL INTEGRATING SINGLE CELL LEVEL TRANSCRIPTOMICS, STATE-OF-THE- ART BEHAVIOR METHODS IN HIV TG AND WILD-TYPE RATS, AND COMPUTATIONAL STRATEGIES FOR THE DECONVOLUTION OF THE GENE REGULATORY NETWORK AT THE SINGLE CELL LEVEL WILL ELUCIDATE KEY MECHANISMS THAT UNDERLIE THE EFFECTS OF HIV AND OPIOID ABUSE AND THEIR DETRIMENTAL INTERACTIONS ON NEUROHIV PROGRESSION, VIRUS EXPRESSION AND PERSISTENCE. THE RESULTS WILL INDICATE TRANSFORMATIVE NEW MECHANISTIC HYPOTHESES THAT MAY LEAD TO NOVEL THERAPEUTIC CONCEPTS FOR OPIOID USE DISORDER (OUD) IN THE SETTING OF HIV AND WILL ESTABLISH KEY RESOURCES FOR THE NEUROHIV FIELD TO BE MADE PUBLICLY AVAILABLE THROUGH THE SCORCH DATA COORDINATION CENTER AND OTHER PUBLIC REPOSITORIES.

LEADERSHIP IN AD/ADRD DRUG DISCOVERY - SUMMARY THIS R35 LEADERSHIP APPLICATION IS RELEVANT TO MILESTONE 6D OF THE GOALS/MILESTONES OF THE NIH ALZHEIMER’S DISEASE AND ALZHEIMER’S DISEASE RELATED DEMENTIAS (AD/ADRD) SUMMITS—“INITIATE DRUG DISCOVERY EFFORTS TO DEVELOP NOVEL THERAPEUTIC AGENTS.” OUR OVERRIDING GOAL IN THIS APPLICATION IS TO SUPPORT THE INFRASTRUCTURE THE PI IS ASSEMBLING FOR AD/ADRD DRUG DISCOVERY AT SCRIPPS RESEARCH, WHICH WILL CONTINUE WELL AFTER THE AWARD IS OVER. OUR MAJOR PLANNED MILESTONE IS AIMED TO INSPIRE PROGRAM BUILDING AND CREATE TEAM BUILDING FOR AD/ADRD DRUG DISCOVERY USING THE VERY CONSIDERABLE INSTITUTIONAL RESOURCES AT SCRIPPS RESEARCH AND ITS CALIBR DRUG DISCOVERY CENTER. WE ARE ALSO BUILDING ONE OF THE NATION’S TOP-RANKED GRADUATE SCHOOL PROGRAMS IN DRUG DISCOVERY VIA OUR MENTORING USING THE FACULTY OF SCRIPPS’ #1/#2-RANKED CHEMISTRY- BIOCHEMISTRY DEPARTMENTS IN THE WORLD. AS PROOF OF FEASIBILITY, OF THE SIX CURRENTLY FDA-APPROVED MEDICINES FOR AD, THREE WERE DEVELOPED OUT OF THE PI, DR. LIPTON’S LABORATORY. VIA THIS R35 LEADERSHIP APPLICATION, DR. LIPTON WILL MENTOR OTHERS TO DEVELOP AD/ADRD-RELATED DRUGS ACTING AT NOVEL TARGETS TOWARD DISEASE-MODIFYING THERAPY. SPECIFICALLY, DR. LIPTON WILL SERVE AS RESEARCH MENTOR FOR NEW INVESTIGATORS AND EARLY STAGE INVESTIGATORS (NI/ESI) IN AD/ADRD DRUG DISCOVERY. TO DATE, VIRTUALLY ALL AD/ADRD THERAPEUTICS EVALUATED IN HUMAN CLINICAL TRIALS HAVE SO FAR FAILED TO SHOW DISEASE-MODIFYING EFFECTS FOR AD/ADRD. FOR EXAMPLE, THE LACK OF SIGNIFICANT EFFICACY IN CLINICAL TRIALS WITH ASS-CENTERED THERAPEUTICS TO DATE DEMANDS A NEW PARADIGM FOR DEVELOPMENT OF EFFECTIVE AD THERAPEUTICS. TO OVERCOME THESE SIGNIFICANT GAPS IN KNOWLEDGE AND TO ADVANCE THERAPIES, IMPROVEMENTS IN THE MODELS AND STRATEGIES BY WHICH AD/ADRD RESEARCHERS FUNCTION AND EXECUTE NEED TO OCCUR. ONE SOLUTION TO THIS CHALLENGE IS TO UNITE THE BEST BASIC SCIENTISTS WITH TRAINING IN NEUROSCIENCE, STRUCTURAL BIOLOGY, BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, WITH EQUALLY EXPERT TEAMS IN THE PHARMACEUTICAL INDUSTRY TRAINED IN HIGH-THROUGHPUT SCREENING, ASSAY DEVELOPMENT, MEDICINAL CHEMISTRY, CHEMICAL BIOLOGY AND PHARMACOLOGY. WITH A COLLECTIVE AND HARMONIZED TEAM ALONG WITH SIGNIFICANT MENTORING EFFORTS FOR JUNIOR FACULTY (NI/ESI), THE PI, DR. LIPTON, HAS INITIATED THREE MAJOR EFFORTS TO ADDRESS THIS UNMET MEDICAL NEED, WHICH WILL BE CARRIED OUT UNDER THE AUSPICES OF THE CURRENT R35 LEADERSHIP AWARD APPLICATION: · INVESTIGATION, IDENTIFICATION AND CHARACTERIZATION OF POTENTIAL AD/ADRD THERAPEUTIC TARGETS IN THE CONTEXT OF THE CENTRAL PATHOPHYSIOLOGICAL PROCESSES IN AD/ADRD. · EXECUTION OF DRUG DISCOVERY CAMPAIGNS TO DEVELOP INVESTIGATIONAL NEW DRUG (IND) CLINICAL CANDIDATES ITERATIVELY WITH THE TARGET ELUCIDATION EFFORTS, WHILE BUILDING UPON SCRIPPS DRUG DISCOVERY INFRASTRUCTURE TO ACCOMPLISH THIS. · CONTINUE TO MENTOR JUNIOR FACULTY AND BUILD A WORLD-CLASS GRADUATE SCHOOL AROUND THE CHEMICAL BIOLOGY OF DRUG DESIGN FOR AD/ADRD AT SCRIPPS (CURRENTLY RANKED #2 BY US NEWS FOR BIOCHEMISTRY).

IMMUNOLOGY TRAINING