PI: smith, James Title: Lead Compound Discovery from Engineered Analogs of Occidiofungin

Received: 09/03/2016 FOA: PA16-303 Council: 01/2017

Competition ID: FORMS-D FOA Title: PHS 2016-02 OMNIBUS SOLICITATION OF THE NIH FOR SMALL 

BUSINESS TECHNOLOGY TRANSFER GRANT APPLICATIONS (PARENT STTR 

[R41/R42])

1 R41 AI131792-01 Dual: Accession Number: 3966533

IPF: 10038489 Organization: SANO CHEMICALS, INC

Former Number: Department: Microbiology

IRG/SRG: ZRG1 BCMB-G (10)B AIDS: N Expedited: N

Subtotal Direct Costs 

(excludes consortium F&A) 

Year 1:

Animals: N 

Humans: N 

Clinical Trial: N

Current HS Code: 10

HESC: N

New Investigator: N

Early Stage Investigator: N

Senior/Key Personnel: Organization: Role Category:

James Smith Ph.D Sano Chemicals PD/PI 

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OMB Number: 4040-0001

Expiration Date: 06/30/2016

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303 . Received Date:

2016-09-03T22:03:46.000-04:00

APPLICATION FOR FEDERAL ASSISTANCE

SF 424 (R&R)

3. DATE RECEIVED BY STATE State Application Identifier

1. TYPE OF SUBMISSION* 4.a. Federal Identifier

❍ Pre-application ● Application ❍ Changed/Corrected

Application

b. Agency Routing Number

2. DATE SUBMITTED Application Identifier

occidiofungin2016

c. Previous Grants.gov Tracking Number

5. APPLICANT INFORMATION Organizational DUNS*: 078514829

Legal Name*: Sano Chemicals

Department: Microbiology

Division: Antibiotics

Street1*:

Street2:

City*:

County:

State*:

Province:

Country*: 

ZIP / Postal Code*: -

Person to be contacted on matters involving this application

Prefix: Dr. First Name*: James Middle Name: Leif Last Name*: Smith Suffix: 

Position/Title: Chief Executive Officer

Street1*: 1000 San Jacinto Ln

Street2:

City*:

County:

State*:

Province:

Country*: 

ZIP / Postal Code*: -

Phone Number*: Fax Number: Email: 

6. EMPLOYER IDENTIFICATION NUMBER (EIN) or (TIN)*

7. TYPE OF APPLICANT* R: Small Business

Other (Specify):

Small Business Organization Type ❍ Women Owned ❍ Socially and Economically Disadvantaged

8. TYPE OF APPLICATION* If Revision, mark appropriate box(es).

● New ❍ Resubmission ❍ A. Increase Award ❍ B. Decrease Award ❍ C. Increase Duration

❍ Renewal ❍ Continuation ❍ Revision ❍ D. Decrease Duration ❍ E. Other (specify) :

Is this application being submitted to other agencies?* ❍Yes ●No What other Agencies?

9. NAME OF FEDERAL AGENCY*

National Institutes of Health

10. CATALOG OF FEDERAL DOMESTIC ASSISTANCE NUMBER

TITLE:

11. DESCRIPTIVE TITLE OF APPLICANT'S PROJECT*

Lead Compound Discovery from Engineered Analogs of Occidiofungin

12. PROPOSED PROJECT

Start Date* Ending Date*

04/01/2017 03/31/2018

13. CONGRESSIONAL DISTRICTS OF APPLICANT

TX-017
Contact PD/PI: Smith, James Leif 

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303 . Received Date:

2016-09-03T22:03:46.000-04:00

SF 424 (R&R) APPLICATION FOR FEDERAL ASSISTANCE Page 2

14. PROJECT DIRECTOR/PRINCIPAL INVESTIGATOR CONTACT INFORMATION

Prefix: Dr. First Name*: James Middle Name: Leif Last Name*: Smith Suffix: Ph.D

Position/Title: Chief Executive Officer

Organization Name*: Sano Chemicals

Department: Microbiology

Division: Antibiotics

Street1*:

Street2:

City*:

County:

State*:

Province:

Country*: 

ZIP / Postal Code*: -

Phone Number*: - - Fax Number: - Email*: 

15. ESTIMATED PROJECT FUNDING

a. Total Federal Funds Requested* $

b. Total Non-Federal Funds* $0.00

c. Total Federal & Non-Federal Funds* $

d. Estimated Program Income* $0.00

16. IS APPLICATION SUBJECT TO REVIEW BY STATE

EXECUTIVE ORDER 12372 PROCESS?*

a. YES ❍ THIS PREAPPLICATION/APPLICATION WAS MADE

AVAILABLE TO THE STATE EXECUTIVE ORDER 12372

PROCESS FOR REVIEW ON:

DATE:

b. NO ● PROGRAM IS NOT COVERED BY E.O. 12372; OR

❍ PROGRAM HAS NOT BEEN SELECTED BY STATE FOR

REVIEW

17. By signing this application, I certify (1) to the statements contained in the list of certifications* and (2) that the statements herein

are true, complete and accurate to the best of my knowledge. I also provide the required assurances * and agree to comply with

any resulting terms if I accept an award. I am aware that any false, fictitious, or fraudulent statements or claims may subject me to

criminal, civil, or administrative penalties. (U.S. Code, Title 18, Section 1001)

● I agree*

* The list of certifications and assurances, or an Internet site where you may obtain this list, is contained in the announcement or agency specific instructions.

18. SFLLL or OTHER EXPLANATORY DOCUMENTATION File Name: 

19. AUTHORIZED REPRESENTATIVE

Prefix: Dr. First Name*: James Middle Name: Leif Last Name*: Smith Suffix: 

Position/Title*: Chief Executive Officer

Organization Name*: Sano Chemicals

Department: Microbiology

Division: Antibiotics

Street1*:

Street2:

City*:

County:

State*:

Province:

Country*: 

ZIP / Postal Code*: -

Phone Number*: Fax Number: Email*: 

Signature of Authorized Representative*

James Smith

Date Signed*

09/03/2016

20. PRE-APPLICATION File Name: Mime Type:

21. COVER LETTER ATTACHMENT File Name:1235-CoverLetter.pdf Mime Type: application/pdf
424 R&R and PHS-398 Specific

Table Of Contents Page Numbers

SF 424 R&R Cover Page----------------------------------------------------------------------------------------- 1

 Table of Contents------------------------------------------------------------------------- 3

Performance Sites--------------------------------------------------------------------------------------------- 4

Research & Related Other Project Information------------------------------------------------------------------ 5

 Project Summary/Abstract(Description)----------------------------------------------------- 6

 Project Narrative------------------------------------------------------------------------- 7

 Facilities & Other Resources-------------------------------------------------------------- 8

 Equipment--------------------------------------------------------------------------------- 11

 Other Attachments------------------------------------------------------------------------- 13

 1241-SBC_000701469---------------------------------------------------- 13

Research & Related Senior/Key Person-------------------------------------------------------------------------- 14

Research & Related Budget Year - 1---------------------------------------------------------------------------- 19

Budget Justification------------------------------------------------------------------------------------------ 22

Research & Related Cumulative Budget-------------------------------------------------------------------------- 23

Research & Related Budget - Consortium Budget (Subaward 1)---------------------------------------------------- 24

Total Direct Costs Less Consortium F&A------------------------------------------------------------------------ 29

SBIR STTR Information----------------------------------------------------------------------------------------- 30

PHS398 Cover Page Supplement---------------------------------------------------------------------------------- 32

PHS 398 Research Plan----------------------------------------------------------------------------------------- 34

 Specific Aims----------------------------------------------------------------------------- 35

 Research Strategy------------------------------------------------------------------------- 36

 Bibliography & References Cited----------------------------------------------------------- 42

 Letters of Support------------------------------------------------------------------------ 44

 Resource Sharing Plan(s)------------------------------------------------------------------ 45

 

Contact PD/PI: Smith, James Leif 

Table of Contents Page 3
	
Contact PD/PI: Smith, James Leif 

OMB Number: 4040-0010

Expiration Date: 06/30/2016

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303. Received Date:

2016-09-03T22:03:46.000-04:00

Project/Performance Site Location(s)

Project/Performance Site Primary Location ❍ I am submitting an application as an individual, and not on behalf of

a company, state, local or tribal government, academia, or other type of

organization.

Organization Name: Sano Chemicals

Duns Number:

Street1*:

Street2:

City*:

County:

State*:

Province:

Country*:

Zip / Postal Code*:

Project/Performance Site Congressional District*: TX-017

Project/Performance Site Location 1 ❍ I am submitting an application as an individual, and not on behalf of

a company, state, local or tribal government, academia, or other type of

organization.

Organization Name: Texas A&M University

DUNS Number:

Street1*:

Street2:

City*:

County:

State*:

Province:

Country*:

Zip / Postal Code*:

Project/Performance Site Congressional District*: TX-017

File Name Mime Type

Additional Location(s)

 Page 4 
Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303. Received Date:

2016-09-03T22:03:46.000-04:00

OMB Number: 4040-0001

Expiration Date: 06/30/2016

RESEARCH & RELATED Other Project Information

1. Are Human Subjects Involved?* ❍ Yes ● No

1.a. If YES to Human Subjects

 Is the Project Exempt from Federal regulations? ❍ Yes ❍ No

If YES, check appropriate exemption number: 1 2 3 4 5 6

If NO, is the IRB review Pending? ❍ Yes ❍ No

IRB Approval Date:

Human Subject Assurance Number

2. Are Vertebrate Animals Used?* ❍ Yes ● No

2.a. If YES to Vertebrate Animals

Is the IACUC review Pending? ❍ Yes ❍ No

IACUC Approval Date:

Animal Welfare Assurance Number

3. Is proprietary/privileged information included in the application?* ❍ Yes ● No

4.a. Does this project have an actual or potential impact - positive or negative - on the environment?* ❍ Yes ● No

4.b. If yes, please explain:

4.c. If this project has an actual or potential impact on the environment, has an exemption been authorized or an

environmental assessment (EA) or environmental impact statement (EIS) been performed?

❍ Yes ❍ No

4.d. If yes, please explain:

5. Is the research performance site designated, or eligible to be designated, as a historic place?* ❍ Yes ● No

5.a. If yes, please explain:

6. Does this project involve activities outside the United States or partnership with international

collaborators?*

❍ Yes ● No

6.a. If yes, identify countries:

6.b. Optional Explanation:

Filename

7. Project Summary/Abstract* 1236-projectsummary.pdf

8. Project Narrative* 1237-ProjectNarrative.pdf

9. Bibliography & References Cited 1238-References.pdf

10.Facilities & Other Resources 1239-FacilitiesAndOtherResources.pdf

11.Equipment 1240-Equipment.pdf

12. Other Attachments 1241-SBC_000701469.pdf

Contact PD/PI: Smith, James Leif 

 Page 5
	
Project Summary 

Occidiofungin is a cyclic nonribosomally synthesized antifungal peptide with submicromolar 

fungicidal activity against a broad spectrum of fungi. Occidiofungin is produced by the Gramnegative bacterium Burkholderia contaminans. From our structural characterization studies, 

occidiofungin was determined to have a unique chemical composition. Our studies have also 

revealed that occidiofungin has a novel mechanism of action. Occidiofungin is a potent 

antifungal against fluconazole and caspofungin-resistant Candida albicans. Occidiofungin 

triggers cell death by inducing apoptosis in yeast cells. Occidiofungin has minimal toxicity in 

mice dosed with 2 mg/kg in a 28 day toxicity study. Furthermore, occidiofungin was shown to 

reduce Candida glabrata load in the kidneys of infected mice. All these studies point to the need 

to further the preclinical development of this novel compound. A major need for furthering 

investigational studies on this unique antifungal compound is the identification of a lead 

molecule for preclinical testing. The goal of this application is to screen a library of natural and 

semi-synthetic analogs of occidiofungin for bioactivity testing. The compound that has the best 

properties will be used in the required preclinical tests that are compulsory before our initial 

meeting with the FDA. This work is necessary for furthering additional studies aimed at 

developing the antifungal compound as a new therapeutic. 

 

Contact PD/PI: Smith, James Leif 

Project Summary/Abstract Page 6
	
Project Narrative 

The proposal addresses the need for the development of a novel broad spectrum 

antifungal for the treatment of systemic fungal infections. We will isolate natural analogs 

and produce semi-synthetic analogs of the antifungal occidiofungin. This works is 

essential for identifying a lead compound for preclinical studies that are needed for filing 

an Investigational New Drug (IND) application. 

 

Contact PD/PI: Smith, James Leif 

Project Narrative Page 7
	
Facilities and Other Resources –Sano Chemicals 

Laboratory: 

Sano Chemicals’ laboratories are located approximately 9 miles from the campus of Texas A&M University. 

Sano Chemicals has fully equipped microbiology, molecular biology and chemistry laboratories occupying 

approximately 1,5000 square feet. The laboratories provide ample space for assorted large and small 

equipment and can accommodate up to 15 total investigators and supporting staff. 

Clinical: 

Not Applicable 

Animal: 

Not Applicable 

Computer: 

Sano Chemicals has high speed internet access. Sano Chemicals has a central server with over 15 work 

stations, all of which are protected by appropriate firewalls under the direction of a highly qualified 

administrative consultant. 

Office: 

Sano Chemicals’ administrative offices are located in the Sano Chemicals facility, and occupy approximately 

300 square feet. Sano Chemicals has a 350 square feet conference room used for regular meetings. The 

laboratories have eight computer working stations that can be used by the investigators. 

Other Resources: 

Sano Chemicals is located 9 miles from Texas A&M University and has access to state of the art research core 

facilities. Sano Chemicals has established relationship with The Research Valley Partnership, Texas Triangle 

Regional Center of Innovation and Commercialization, Texas A&M System Technology Commercialization, 

and the Center for New Ventures & Entrepreneurship at Texas A&M. These resources provide a rich 

environment for our company. 

Facilities and Other Resources –Texas A&M University 

Environment – Contribution to Success 

Biology Department has 45 tenured and tenure-track faculty members. Six of the faculty members have well 

established careers in Microbiology. The Department of Biology promotes a supportive environment among 

faculty. Texas A&M University is a world class research and education institution. The university provides a 

rich environment promoting faculty interaction and collaboration. Texas A&M University supports seminars 

and social functions that enhance the research and educational environment, as well as provide and support 

outstanding facilities for cutting edge research. 

Texas A&M University, Shared Facilities: (http://biophysics.tamu.edu/facilities.html)

X-ray Crystallography Laboratory and Center for Structural Biology

The X-ray Laboratory contains the newest X-ray diffraction instruments, high-speed computers and many 

graphics workstations. The Laboratory also provides training for macromolecular structural biology. Consistent 

with this goal, this laboratory organizes seminars, workshops, and always maintains an "open-door" policy for 

equipment use and training. 

Biomolecular NMR Facilities

The Biomolecular NMR Laboratory is located in the Biochemistry Building and houses 500 MHz and 600 MHz 

Varian Inova NMR spectrometers. Both 500 and 600 MHz spectrometers are dedicated to performing all 

multidimensional, multinuclear NMR experiments required to solve the solution structures of proteins and 

nucleic acids (RNA and DNA), as well as probe the conformational dynamics and residue-specific energetics of 

biomolecules and macromolecular complexes. In addition, the NMR Laboratory in the Department of Chemistry 

contains three 500 MHz Varian spectrometers, one 400 MHz instrument, and several low-field instruments. 

 

Contact PD/PI: Smith, James Leif 

Facilities & Other Resources Page 8
	
Each of the NMR facilities is overseen by a full-time NMR laboratory manager who is available to assist and 

train students in modern NMR techniques.

Microscopy and Imaging Center

The Microscopy and Imaging Center provides training and support services for current and emerging 

technologies involving microscopy and related imaging, sample preparation, in situ analysis and digital image 

processing. Several electron and light microscopes are available for use, including: a JEOL JEM-2010 highresolution transmission electron microscope, a JEOL JSM-6400 scanning electron microscope, an ESEM E-3 

environmental SEM, and a Zeiss Axiophot light microscope equipped for bright field, phase contrast, 

fluorescence, and Normarski differential interference contrast microscopy. An increasing number of 

instruments is being interfaced to the latest data collection and analysis/processing hardware and software. 

Laboratory for Biological Mass Spectrometry (LBMS) 

This laboratory provides modern mass spectrometry capabilities to researchers focused on the identification 

and characterization of biomolecules. The research activities of the LBMS include fundamental ion chemistry 

and developmental mass spectrometry, as well as mass spectrometry applications. Research in this laboratory 

provides the underpinning for developing new methods and mass spectrometry instrumentation, and these 

developments are tested and evaluated by collaborations with biological researchers in advance of 

commercialization. 

Fluorescence Spectroscopy

The extensive fluorescence capabilities available at TAMU include ten photon-counting spectrofluorimeters, 

many using laser excitation, for steady-state or time-resolved measurements, in addition to a femtosecond 

mode-locked titanium-sapphire laser and inverted microscope suitable for fluorescence correlation 

spectroscopy and other fluorescence measurements. These instruments use either single- or multi-photon 

excitation to measure, among many other things, rates of macromolecular tumbling, distances between 30 and 

100Å by fluorescence resonance energy transfer, the rates of reactions associated with individual molecules, 

and the kinetics and thermodynamics of macromolecular associations or receptor-ligand bindings. 

Laboratory for Molecular Simulation

This facility brings molecular modeling and computational chemistry closer to the experimental scientist by 

offering advanced training and assistance to those who already use these tools in their research, and 

beginning training to those who have not yet adopted them. For this purpose, the LMS offers various 

workshops on topics such as UNIX operating systems, as well as the theoretical background and practical 

applications of molecular modeling. Advanced modeling software is available to use mathematical methods to 

calculate the properties of individual molecules, solids, and liquids. 

Paramagnetic Resonance Facility

Paramagnetic probes can provide windows of observation into the structure and dynamics of biological 

systems. The Electron Paramagnetic Resonance (EPR) facility has Bruker X-band EPR capabilities with 

variable temperature control down to liquid helium (4.2¡ K) temperatures. A specialty ENDOR (electron nuclear 

double resonance) instrument operating at Q-band and pumped helium (1.8¡ K) temperatures also is available. 

Associated with these techniques is a fast freeze-quench system that allows trapping of potential intermediates 

in catalytic pathways. 

ITC and DSC Microcalorimetry

Isothermal titration calorimetry (ITC) and Differential Scanning Calorimetry (DSC) are thermodynamic 

techniques for directly measuring the heat absorbed or released during molecular reactions. Our MicroCal 

MCS-ITC, VP-ITC, and VP-DSC instruments allow ultrasensitive characterizations of protein and nucleic acid 

unfolding, protein-ligand binding, protein-nucleic acid interactions, and metal ion binding to metalloproteins. 

Analytical Ultracentrifugation (AUC)

AUC is an essential tool in determining molecular size in complex biological solutions. This can be used to 

provide information about a wide range of systems, from transcriptional activation complexes to the 

oligomerization state of biologically active proteins. We currently have a Beckman Optima XL-A centrifuge 

equipped with absorption optics. 

 

Contact PD/PI: Smith, James Leif 

Facilities & Other Resources Page 9
	
Protein Chemistry Laboratory

The Protein Chemistry Laboratory provides instrumentation and skilled professional staff for the purification 

and microanalysis of proteins and peptides. In addition to teaching state-of-the-art protein chemical techniques 

to students, staff, and faculty, the laboratory offers a variety of analytical and consulting services, including the 

development of new approaches and protocols for advanced technology in protein characterization and 

analysis. 

Institutional Commitment 

Dr. James L. Smith has a 9 mo tenure–track position. Teaching obligations are 1.5 classes per year. He 

will teach a General Microbiology class in the Fall and team-teach a graduate level course on Antimicrobial 

Agents in the Spring semester. He is expected to devote 50% of his effort to research. His start up package 

provided him ample resources to begin his research program, but he is expected to maintain his research 

program through extramural funding. The department has a mentoring program for assistant and associate 

professors. Dr. Smith has two well-established professors, Richard Gomer and Ry Young, as his department 

mentors. Biology Department has a seminar series that brings in investigators that will enrich Dr. Smith’s 

exposure to cutting edge research. The department is committed to maintaining Dr. Smith's international 

reputation. 

Facilities:

Laboratory 

Dr. Smith, laboratory is ~1000 square feet. His lab is equipped and approved for BSL-2 laboratory work and is 

equipped with the necessary molecular biology, protein expression, and protein purification tools necessary to 

conduct the proposal. 

Office:

Dr. Smith has ~250 square feet of office space. Administrative and secretarial support staff is provided for 

faculty within the department. 

Computer

Dell Desktop and Toshiba laptop computers with current operating systems and office application software. 

Department of Biological Science Resources

There are shared instrument facilities on each floor of the Department of Biological Science buildings BSBE 

and BSBW that include centrifuges, -80 C freezers, cold rooms, deionized water, gel documentation, 

nanodrop spectrophotometers, and autoclaves. The department has the following support staff and facilities: 

Computing, Departmental Stockroom, Gene Technologies Laboratory, Instrumentation Shop, Microscopy and 

Imaging Center, and a Safety Office. 

 

Contact PD/PI: Smith, James Leif 

Facilities & Other Resources Page 10
	
Sano Chemicals 

Equipment located in the Sano Chemicals R&D facility that will be used for the project: 

 biosafety cabinet (Class II) 

 ultralow freezer (Nuaire) 

 -20 freezer 

 Oven 

 environmental shaker (New Brunswick) 

 3 New Brunswick Celligen Bioreactor (5 L) 

 UV/Vis Spectrophotometer (Jenway) 

 pH meter (Denver) 

 electrophoresis power supplies 

 agarose and polacrylamide electrophoresis apparatus (BioRad) 

 UVP Dual Intensity Transilluminator 

 (2) polymerase chain reaction icycler (BioRad and MJ Research) 

 microtiter plate reader (BioRad) 

 refrigerated water bath (Haake) 

 (2) 2L water baths (VWR) 

 vortexes 

 teflon vacuum pump 

 microbiological Incubators 180 Liter 

 rocker and a variable rotator 

 heated stir plates 

 sonifier-Energy sonicator 

 (2) refrigerated centrifuges with assorted rotors (Beckman) 

 speedvac (Jouan) 

 lyophilizer (Virtis) 

 autoclave Pelton and Crane (Magnaclave) 

 cold room 

 5ft Chemical Hood (One Point Solution) 

 analytical balance (120/0.0001 grams) 

 digital balances 

 benchtop variable speed centrifuges (Asteria and Eppendorf) 

 4 Dell computers. 

 LCMS System, Thermo Scientific TSQ Quantum Access with HESI Probe with Agilent Front 

End with Binary Pump and variable wavelength detector 

Investigators Equipment 

Texas A&M University - Dr. Smith

The equipment located in Dr. Smith’s laboratory includes: 

 Bio-Rad cell and mini trans blot apparatus 

 Bio-Rad wide and mini sub-cell GT system for DNA electrophoresis and two power supplies for 

protein electrophoresis, westerns, and DNA electrophoresis 

 Two BioRad iCycler with the gradient upgrades 

 BioRad HPLC DuoFlow F10 series with a Quadtec UV detection 

 Carter 4/6 Peristaltic pump 

 Virtis Benchtop Lyophilizer ZL 

 Buchi Rotovap 

 Speedvac 

 Benchtop shaker incubator 

 Sorval RC-5B superspeed refrigerated floor centrifuge 

 Bio-Rad GelDoc XR+ with ImageLab software 

 5ft Labconco Biosafety cabinet, 

 

Contact PD/PI: Smith, James Leif 

Equipment Page 11
	
 5ft Chemical Hood 

 Three Eppendorf benchtop centrifuges 

 VWR Oven Gravity Medium 

 Bio-Rad SmartSpec Plus Spectrophotometer 

 Bio-Rad Gene Pulser XCell 

 Bio-Rad xMark Microplate Absorbance Spectrophotometer 

 Metler Toledo pH meter 

 Oasis balance and analytical balance 

 Two 2L water baths 

 15 L water Bath 

 rocker and a variable rotator 

 Two Genie vortexes 

 Teflon vacuum pump 

 Two Corning heater and stirrers 

 Benchtop shaker incubator 

 Sonifier-Energy sonicator 

 -20 freezer 

 45 cuft Chromatography refrigerator 

 Sanyo V.I.P. Series Space Saving Ultra-Low Freezer 

 Two Percival Biological Incubator Model I-36NL 

 Isotemp 5 cuft incubator 

 Thermo Mega Pure Glass Still 

 3 Dell Computers. 

Departmental Resources

All ultralow freezers are on a central freezer alarm system, 2 autoclaves on same floor as my lab are checked 

weekly for proper maintenance, DNA sequencing facility, and laboratory grade water (deionized and distilled). 

The Microscopy Center is located within the Department of Biological Sciences. It is fully equipped for 

conventional transmission and scanning electron microscopy and confocal laser scanning microscopy. 

Texas A&M Protein Chemistry Lab

The LSBI was established in 2001 and is a core facility for major instrumentation. Equipment at the LSBI is 

available for all TAMU faculty, and it is located less than a 10 minute walk from the Biological Science Building 

BSBE. The facility is equipped with protein sequencing and mass spectrometry resources. 

Biomolecular NMR Facilities

The Biomolecular NMR Laboratory is located in the Biochemistry Building and houses 500 MHz and 600 MHz 

NMR spectrometers. Both 500 and 600 MHz spectrometers are dedicated to performing all multidimensional, 

multinuclear NMR experiments required to solve the solution structures of proteins and nucleic acids (RNA and 

DNA), as well as probe the conformational dynamics and residue-specific energetics of biomolecules and 

macromolecular complexes. In addition, the NMR Laboratory in the Department of Chemistry contains three 

500 MHz spectrometers. Each of the NMR facilities is overseen by a full-time NMR laboratory manager who is 

available to assist and train students in modern NMR techniques. 

 

Contact PD/PI: Smith, James Leif 

Equipment Page 12
	
 

Contact PD/PI: Smith, James Leif 

SBIR.gov SBC Registration

Company Information

SBC Control ID SBC_000701469

Company Name Sano Chemicals Inc

Address 606 Coachlight CT

City College Station State TX Zip 77845

TIN/EIN DUNS

Company URL sanochemicals.com

Number of Employees 6

Is this SBC majority-owned by multiple venture capital operating

companies, hedge funds, or private equity firms?

No

What percentage (%) of the SBC is majority-owned by multiple venture

capital operating companies, hedge funds, or private equity firms?

0%

Company data certified as of February 28, 2015 | U.S. Small Business Administration | SBIR.gov

1241-SBC_000701469 Page 13 
Contact PD/PI: Smith, James Leif 

OMB Number: 4040-0001

Expiration Date: 06/30/2016

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303 . Received Date:

2016-09-03T22:03:46.000-04:00

RESEARCH & RELATED Senior/Key Person Profile (Expanded)

PROFILE - Project Director/Principal Investigator

Prefix: Dr. First Name*: James Middle Name Leif Last Name*: Smith Suffix: Ph.D

Position/Title*: Chief Executive Officer

Organization Name*: Sano Chemicals

Department: Microbiology

Division: Antibiotics

Street1*:

Street2:

City*:

County:

State*:

Province:

Country*:

Zip / Postal Code*:

Phone Number*:  Fax Number: 

E-Mail*: 

Credential, e.g., agency login: 

Project Role*:  PD/PI Other Project Role Category: 

Degree Type:  PhD Degree Year:  2002

Attach Biographical Sketch*:             File Name: 1247-SmithBiosketch.pdf

Attach Current & Pending Support:   File Name:

 Page 14 
 

OMB No. 0925-0001 and 0925-0002 (Rev. 10/15 Approved Through 10/31/2018) 

BIOGRAPHICAL SKETCH 

Provide the following information for the Senior/key personnel and other significant contributors. 

Follow this format for each person. DO NOT EXCEED FIVE PAGES.

NAME: James Leif Smith

eRA COMMONS USER NAME (credential, e.g., agency login): 

POSITION TITLE: Chief Executive Officer and Associate Professor

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, 

include postdoctoral training and residency training if applicable. Add/delete rows as necessary.)

INSTITUTION AND LOCATION

DEGREE

(if 

applicable)

Completion 

Date

MM/YYYY

FIELD OF STUDY

University of Florida, Gainesville, FL Ph.D. 08/2002

College of Medicine’s 

Multidisciplinary 

Program, Microbial 

Genetics and Protein 

Chemistry

University of Florida, Gainesville, FL MBA 08/2002 Finance and 

Competitive Strategy

Oragenics Inc., Alachua, FL Postdoctoral 05/2006 Antimicrobial 

Development

A. Personal Statement 

Infectious diseases are still the second leading cause of death worldwide. Septicemia alone accounts for 

nearly 30,000 deaths per year in the United States. I am committed to finding avenues to minimize the 

suffering of those who desperately need alternatives to conventional therapy. My strength in this area of 

research lies in my cross disciplinary background, which encompasses bacterial cultivation, bacterial genetics, 

process biochemistry, and biophysical applications such as NMR and Mass Spectrometry. As a postdoctoral 

fellow at Oragenics Inc, I gained considerable amount of experience under the guidance of the distinguished 

microbiology professor Dr. Jeffrey D. Hillman. Dr. Jeffrey Hillman founded Oragenics to commercialize the 

fruits of 25 years of research at Harvard and the University of Florida. It was here that I expanded my 

knowledge of Microbiology and learned several molecular, proteomic, and animal handling techniques. I have 

developed several scientific programs while at Oragenics, one of which was the development of novel 

antibiotics. Since leaving Oragenics in 2006, I have successfully built my own research program around 

isolating, identifying, and characterizing novel antimicrobials. Our group laid the ground work, i.e. production, 

purification and the structural activity determination of mutacin 1140, for the future studies aimed at 

understanding the compounds activity. Synthesis of novel structural variants of mutacin 1140 with enhanced 

bioactivities have reinvigorate the development of the compound for treating Gram-positive bacterial infections. 

My work over the last seven years on a novel antifungal compound named occidiofungin has been equally as 

fulfilling. The project has a good potential for development of a new drug for the treatment of serious fungal 

infections. I am eager to put my knowledge and experience toward the therapeutic development of 

occidiofungin. 

Contact PD/PI: Smith, James Leif 

Biosketches Page 15 
B. Positions and Honors 

Positions and Employment

August 1996 – August 2002 

Graduate Research Assistant, College of Medicine, University of Florida 

September 2002 – May 2006 

Postdoctoral/Project Leader, Antimicrobial Division, Oragenics, Inc. 

August 2006 – June 2010 

Assistant Professor, Department of Biological Sciences and Department of Basic Sciences at the 

College of Veterinary Medicine, Mississippi State University 

July 2010 – August 2013 

Assistant Professor, Department of Biological Sciences, Texas A&M University 

March 2012 - present 

Chief Executive Officer, Sano Chemicals 

August 2013 – present 

Associate Professor, Department of Biological Sciences, Texas A&M University 

Other Experience

February 1999 – March 2004, 

Director and Treasurer, The Able Trust, 106 East College Avenue, Suite 820, Tallahassee, FL 32301 

Served on the Finance Committee (Chairman), Executive Committee, and the By-laws Committee 

October 2009 – October 2010 

Guest-Editor, Current Pharmaceutical Biotechnology , Special topics issue will be centered on the 

importance of antimicrobial research for promoting our understanding of microbial physiology. 

Honors

December, 2007 

National High Magnetic Field Laboratory, Winter 2007-2008 issue of Mag Lab Reports., Science Starts 

Here, Featured as an Upcoming Scientist. 

March, 2009 

Smith J. L., Dahal, N., Wilson-Stanford S., Application number US PPA 61/273,403; Small Peptide 

Induction Technology 

April, 2009 

Hillman J. D., Orugunty R. S., and Smith J. L., Application number US Utility Patent 7,521,529; 

Synthesis of differentially protected orthogonal lanthionines 

May, 2009, 

 Invited Speaker, Finnish Biosciences Conference, Helsinki, Finland

May, 2009 

Lu S, Smith J. L., Austin F., and Gu Ganyu, Application number US PPA 61/217,026; Occidiofungin, a 

Unique Glycopeptide Produced by a Strain of Burkholderia contaminans 

October, 2009 

Smith J. L., and Orugunty R. S., Application number US Utility 12/589,115.Functional Enhancement of 

Antimicrobials 

 

Contact PD/PI: Smith, James Leif 

Biosketches Page 16
	
November 2009, 

Charles C. Randall Lectureship Award of the South Central Branch of the American Society for 

Microbiology 

July 2010 

Lu S, Smith J. L., Austin F., and Gu G., US Utility Patent 20110136729; WO 2010/138173; 

Occidiofungin, a Unique Glycopeptide Produced by a Strain of Burkholderia contaminans 

September 2012 

Smith J.L., Wilson-Stanford S., Hillman J.D., US PPA 61/603,661; Variants of the Lantibiotic MU1140 

and Other Lantibiotics with Improved Pharmacological Properties and Structural Features 

September 2012 

Smith J.L., Wilson-Stanford S., Hillman J.D., US PPA 61/603,693; Improved Replacement Therapy 

for Dental Caries 

September 2013 

 Editorial Board Member for Applied and Environmental Microbiology 

C. Contribution to Science 

1. The study of antimicrobials may lead to life-saving therapies and help ensure a sustainable food supply. 

This in itself is enough to motivate my research efforts. However, there is more to antimicrobial research. This 

work also leads to a better understanding of microbial physiology and the complexity of the processes that 

microorganisms undergo to maintain a sustainable niche. I have focused my research efforts towards enabling 

a better understanding of peptide-based antibiotics, particularly on lantibiotics and a novel antifungal peptide 

named occidiofungin. Novel peptide-based antimicrobials are of great interest to my group. Whether 

ribosomally or non-ribosomally synthesized, peptide-based antimicrobial compounds often contain complex 

structures and biosynthetic systems. The discovery of unique structures, and determination of their roles in 

antimicrobial function, is a fascinating area of research. We have characterized the structure of the Grampositive active antibiotic mutacin 1140 and the broad spectrum antifungal occidiofungin. The identification and 

bioactivity characterization of these antibiotics has been the basis for the development of these natural 

products for the treatment of serious bacterial and fungal diseases. 

a. Gu G, Smith L, Liu A, Lu SE. Genetic and biochemical map for the biosynthesis of occidiofungin, an 

antifungal produced by Burkholderia contaminans strain MS14. Appl Environ Microbiol. 2011 

Sep;77(17):6189-98. doi: 10.1128/AEM.00377-11. Epub 2011 Jul 8. PubMed PMID: 21742901; PubMed 

Central PMCID: PMC3165383. 

b. Lu SE, Novak J, Austin FW, Gu G, Ellis D, Kirk M, Wilson-Stanford S, Tonelli M, Smith L. Occidiofungin, 

a unique antifungal glycopeptide produced by a strain of Burkholderia contaminans. Biochemistry. 2009 

Sep 8;48(35):8312-21. doi: 10.1021/bi900814c. PubMed PMID: 19673482; PubMed Central PMCID: 

PMC2771368. 

c. Smith L, Zachariah C, Thirumoorthy R, Rocca J, Novák J, Hillman JD, Edison AS. Structure and 

dynamics of the lantibiotic mutacin 1140. Biochemistry. 2003 Sep 9;42(35):10372-84. PubMed PMID: 

12950164.

d. Smith L, Novák J, Rocca J, McClung S, Hillman JD, Edison AS. Covalent structure of mutacin 1140 and 

a novel method for the rapid identification of lantibiotics. Eur J Biochem. 2000 Dec;267(23):6810-6. 

PubMed PMID: 11082191. 

2. Gaining an understanding of the coordinated function of the enzymes leading to their production is equally 

as interesting, because of the potential for manipulating these enzymes for synthesizing and engineering 

unique compounds. Mutacin 1140 is post-translationally modified and we have furthered the understanding of 

the coordinated interaction of the PTM enzyme function during the synthesis of mutacin 1140. Furthermore, we 

have furthered our understanding of the biosynthesis of the non ribosomally synthesized antifungal 

occidiofungin. These studies provide a basis for manipulating the biosynthetic pathway for producing novel 

analogs of these compounds. 

 

Contact PD/PI: Smith, James Leif 

Biosketches Page 17
	
 

a. Escano J, Stauffer B, Brennan J, Bullock M, Smith L. Biosynthesis and Transport of the Lantibiotic 

Mutacin 1140 Produced by Streptococcus mutans. J Bacteriol. 2015 Apr 1;197(7):1173-84. doi: 

10.1128/JB.02531-14. Epub 2015 Jan 20. PubMed PMID: 25605307. 

b. Escano J, Stauffer B, Brennan J, Bullock M, Smith L. The leader peptide of mutacin 1140 has distinct 

structural components compared to related class I lantibiotics. Microbiologyopen. 2014 Dec;3(6):961-72. 

doi: 10.1002/mbo3.222. Epub 2014 Nov 17. PubMed PMID: 25400246; PubMed Central PMCID: 

PMC4263518. 

c. Chen S, Wilson-Stanford S, Cromwell W, Hillman JD, Guerrero A, Allen CA, Sorg JA, Smith L. Sitedirected mutations in the lanthipeptide mutacin 1140. Appl Environ Microbiol. 2013 Jul;79(13):4015-23. 

doi: 10.1128/AEM.00704-13. Epub 2013 Apr 19. PubMed PMID: 23603688; PubMed Central PMCID: 

PMC3697549. 

d. Ravichandran A, Gu G, Escano J, Lu SE, Smith L. The presence of two cyclase thioesterases expands 

the conformational freedom of the cyclic Peptide occidiofungin. J Nat Prod. 2013 Feb 22;76(2):150-6. doi: 

10.1021/np3005503. Epub 2013 Feb 8. PubMed PMID: 23394257; PubMed Central PMCID: 

PMC4142711. 

3. During my time at Oragenics Inc., I learned the methods used to optimize the production and purification of 

antimicrobial compounds. I continued some of these studies when I first began as an assistant professor. I 

have developed methods to extract the antibiotic mutacin 1140 from complex media and enabled the 

antibiotics production in minimal media. These methods have been translated over to Oragenics Inc, which is 

developing mutacin 1140 for the treatment of Clostridium difficile infections. 

a. Dahal N., Chaney N., Ellis D, Lu S., Smith L. Optimization of the Production of the Lantibiotic Mutacin 

1140 in Minimal Media. Process Biochem. 2010 Jul 1;45(7):1187-1191. PubMed PMID: 20711515; 

PubMed Central PMCID: PMC2918913. 

b. Chaney N, Wilson-Stanford S, Kastrantas J, Dahal N, Smith L. Rapid method for extracting the antibiotic 

mutacin 1140 from complex fermentation medium yeast extract. Can J Microbiol. 2009 Nov;55(11):1261-

6. doi: 10.1139/w09-091. PubMed PMID: 19940934. 

Complete List of Published Work in MyBibliography:

http://www.ncbi.nlm.nih.gov/sites/myncbi/10WFtnmKHuo55/bibliography/47767237/public/?sort=date&direction

=ascending

D. Research Support

Current Research Support

Agency: NIH-NIAID 

Award 1R41AI122441-01A1 

Principal Investigator: James L. Smith 

Duration: 04/01/2016 – 3/31/2018 

Proposal Title: Optimization of the Production and Isolation of the Novel Antifungal Occidiofungin 

Completed Research Support

 

Contact PD/PI: Smith, James Leif 

Biosketches Page 18 
OMB Number: 4040-0001

Expiration Date: 06/30/2016

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303 . Received Date: 2016-09-03T22:03:46.000-04:00

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  1

ORGANIZATIONAL DUNS*:   

Budget Type*: ● Project ❍ Subaward/Consortium

Enter name of Organization: Sano Chemicals

Start Date*: 04-01-2017 End Date*: 03-31-2018 Budget Period: 1

A. Senior/Key Person

# Prefix First Name* Middle

Name

Last Name* Suffix Project Role* Base

Salary ($)

Calendar

Months

Academic

Months

Summer

Months

Requested

Salary ($)*

Fringe

Benefits ($)*

Funds Requested ($)*

1 . Dr. James Leif Smith Ph.D PD/PI 0.60

2 . Dr. Akshaya Ravichandran Research

Scientist

12.00

Total Funds Requested for all Senior Key Persons in the attached file

Additional Senior Key Persons: File Name: Total Senior/Key Person

Mime Type:

B. Other Personnel

Number of

Personnel*

Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)*

Total Number Other Personnel Total Other Personnel

Total Salary, Wages and Fringe Benefits (A+B)

RESEARCH & RELATED Budget {A-B} (Funds Requested)

Contact PD/PI: Smith, James Leif 

 Page 19
	
Contact PD/PI: Smith, James Leif 

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303 . Received Date:

2016-09-03T22:03:46.000-04:00

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 1

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project ❍ Subaward/Consortium

Organization: Sano Chemicals

Start Date*: 04-01-2017 End Date*: 03-31-2018 Budget Period: 1

C. Equipment Description

List items and dollar amount for each item exceeding $5,000

Equipment Item Funds Requested ($)*

Total funds requested for all equipment listed in the attached file

Total Equipment

Additional Equipment: File Name:

Mime Type:

D. Travel Funds Requested ($)*

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 0.00

2. Foreign Travel Costs 0.00

Total Travel Cost 0.00

E. Participant/Trainee Support Costs Funds Requested ($)*

1. Tuition/Fees/Health Insurance 0.00

2. Stipends 0.00

3. Travel 0.00

4. Subsistence 0.00

5. Other: 

 Number of Participants/Trainees Total Participant Trainee Support Costs 0.00

RESEARCH & RELATED Budget {C-E} (Funds Requested)

 Page 20 
Contact PD/PI: Smith, James Leif 

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303 . Received Date:

2016-09-03T22:03:46.000-04:00

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 1

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project ❍ Subaward/Consortium

Organization: Sano Chemicals

Start Date*: 04-01-2017 End Date*: 03-31-2018 Budget Period: 1

F. Other Direct Costs Funds Requested ($)*

1. Materials and Supplies

2. Publication Costs 0.00

3. Consultant Services 0.00

4. ADP/Computer Services 0.00

5. Subawards/Consortium/Contractual Costs

6. Equipment or Facility Rental/User Fees 0.00

7. Alterations and Renovations 0.00

Total Other Direct Costs

G. Direct Costs Funds Requested ($)*

Total Direct Costs (A thru F)

H. Indirect Costs

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)*

1 . MTDC 40.00

Total Indirect Costs

Cognizant Federal Agency

(Agency Name, POC Name, and POC Phone Number)

I. Total Direct and Indirect Costs Funds Requested ($)*

Total Direct and Indirect Institutional Costs (G + H)

J. Fee Funds Requested ($)*

K. Budget Justification* File Name: 1234-BudgetJustificationSano.pdf Mime Type: application/pdf

(Only attach one file.)

RESEARCH & RELATED Budget {F-K} (Funds Requested)

 Page 21 
 Budget Justification - Sano Chemicals 

Statement of Work

Sano Chemicals will perform the work involved in the synthesis of the semi-synthetic 

analogs of occidiofungin. The bioactivity of these analogs will be evaluated at Texas 

A&M university. 

Salaries and Wages 

Principal Investigator: Dr. Smith (5% Effort, 0.6 cal month Effort for year 1). Dr. Smith will 

be actively involved in the day to day activities of the project and will ensure successful 

completion by providing his experience. Furthermore, Dr. Smith will be responsible for 

the overall administration and coordination of the project. 

Research Scientist: Akshaya Ravichandran (100% Effort, 12 cal month Effort for year 1) 

Dr. Ravichandran will have to commit 100% of her time on this project, which is a 

sufficient time commitment for the successful completion of the project. Akshaya has 

over 6 years of experience working with occidiofungin. Her experience will be invaluable 

towards the completion of the genetic modification studies outlined in the proposal. She 

will also work on engineering the semi-synthetic analogs of occidiofungin. 

Equipment

No additional equipment needs for this project. 

Materials and Supplies 

The cost of materials and supplies is based on previous experience with the 

fermentation supplies, molecular biology supplies, and expected analytical fees. 

Molecular reagents and bacterial cultivation supplies will be needed to produce 

occidiofungin analogs, validate, and characterize the products. Commodity funds are 

requested for laboratory supplies including single-use disposable plastic ware such as 

centrifuge tubes, micropipetter tips, pipettes and culture plates; reagents and chemicals 

required for bacterial culture; personal protective equipment such as gloves, safety 

glasses, and masks; and other incidental supplies. 

Travel: 

None Requested 

Indirect Cost Rate 

Indirect costs are computed at the rate of 40% of total modified total direct costs.

 

Contact PD/PI: Smith, James Leif 

Budget Justification Attachment Page 22
	
Contact PD/PI: Smith, James Leif 

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303 . Received Date:

2016-09-03T22:03:46.000-04:00

RESEARCH & RELATED BUDGET - Cumulative Budget

Totals ($)

Section A, Senior/Key Person

Section B, Other Personnel

Total Number Other Personnel

Total Salary, Wages and Fringe Benefits

(A+B)

Section C, Equipment

Section D, Travel 0.00

1. Domestic 0.00

2. Foreign 0.00

Section E, Participant/Trainee Support

Costs

0.00

1. Tuition/Fees/Health Insurance 0.00

2. Stipends 0.00

3. Travel 0.00

4. Subsistence 0.00

5. Other

6. Number of Participants/Trainees

Section F, Other Direct Costs

1. Materials and Supplies

2. Publication Costs 0.00

3. Consultant Services 0.00

4. ADP/Computer Services 0.00

5. Subawards/Consortium/Contractual

Costs

6. Equipment or Facility Rental/User

Fees

0.00

7. Alterations and Renovations 0.00

8. Other 1

9. Other 2

10. Other 3

Section G, Direct Costs

(A thru F)

Section H, Indirect Costs

Section I, Total Direct and Indirect Costs

(G + H)

Section J, Fee

 Page 23 
OMB Number: 4040-0001

Expiration Date: 06/30/2016

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303 . Received Date: 2016-09-03T22:03:46.000-04:00

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  1

ORGANIZATIONAL DUNS*:   

Budget Type*: ❍ Project ● Subaward/Consortium

Enter name of Organization: Texas A&M University

Start Date*: 04-01-2017 End Date*: 03-31-2018 Budget Period: 1

A. Senior/Key Person

# Prefix First Name* Middle

Name

Last Name* Suffix Project Role* Base

Salary ($)

Calendar

Months

Academic

Months

Summer

Months

Requested

Salary ($)*

Fringe

Benefits ($)*

Funds Requested ($)*

1 . Dr. James Smith PD/PI 0.60

Total Funds Requested for all Senior Key Persons in the attached file

Additional Senior Key Persons: File Name: Total Senior/Key Person

Mime Type:

B. Other Personnel

Number of

Personnel*

Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)*

Post Doctoral Associates

1 Graduate Students 6.00

Undergraduate Students

Secretarial/Clerical

1 Total Number Other Personnel Total Other Personnel

Total Salary, Wages and Fringe Benefits (A+B)

RESEARCH & RELATED Budget {A-B} (Funds Requested)

Contact PD/PI: Smith, James Leif 

 Page 24
	
Contact PD/PI: Smith, James Leif 

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303 . Received Date:

2016-09-03T22:03:46.000-04:00

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 1

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium

Organization: Texas A&M University

Start Date*: 04-01-2017 End Date*: 03-31-2018 Budget Period: 1

C. Equipment Description

List items and dollar amount for each item exceeding $5,000

Equipment Item Funds Requested ($)*

Total funds requested for all equipment listed in the attached file

Total Equipment

Additional Equipment: File Name:

Mime Type:

D. Travel Funds Requested ($)*

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions)

2. Foreign Travel Costs

Total Travel Cost

E. Participant/Trainee Support Costs Funds Requested ($)*

1. Tuition/Fees/Health Insurance

2. Stipends

3. Travel

4. Subsistence

5. Other: 

 Number of Participants/Trainees Total Participant Trainee Support Costs

RESEARCH & RELATED Budget {C-E} (Funds Requested)

 Page 25 
Contact PD/PI: Smith, James Leif 

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303 . Received Date:

2016-09-03T22:03:46.000-04:00

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 1

ORGANIZATIONAL DUNS*: 0202718260000

Budget Type*: ❍ Project ● Subaward/Consortium

Organization: Texas A&M University

Start Date*: 04-01-2017 End Date*: 03-31-2018 Budget Period: 1

F. Other Direct Costs Funds Requested ($)*

1. Materials and Supplies

2. Publication Costs 0.00

3. Consultant Services 0.00

4. ADP/Computer Services 0.00

5. Subawards/Consortium/Contractual Costs 0.00

6. Equipment or Facility Rental/User Fees

7. Alterations and Renovations 0.00

Total Other Direct Costs

G. Direct Costs Funds Requested ($)*

Total Direct Costs (A thru F)

H. Indirect Costs

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)*

1 . MTDC

Total Indirect Costs

Cognizant Federal Agency

(Agency Name, POC Name, and POC Phone Number)

Arif Karim HHS 2147673261

I. Total Direct and Indirect Costs Funds Requested ($)*

Total Direct and Indirect Institutional Costs (G + H)

J. Fee Funds Requested ($)*

K. Budget Justification* File Name: 1242-BudgetJustificationAM.pdf Mime Type: application/pdf

(Only attach one file.)

RESEARCH & RELATED Budget {F-K} (Funds Requested)

 Page 26 
Budget Justification-Texas A&M 

STATEMENT OF WORK

Texas A&M will perform the work involved in characterizing the bioactivity of each of the natural 

or synthetic analogs of occidiofungin. The generation of some of the amine and the synthetic 

solid phase peptide synthesis analogs of occidiofungin will be done at Texas A&M University. 

PERSONNEL

James Leif Smith, PhD, Principal Investigator (5% Effort, 0,6 cal month Effort; year 1); He will be 

actively involved in the day to day activities of the project and will ensure successful completion 

by providing his experience. He will oversee the efforts of his research scientist on the project 

and will be actively involved in training and day to day trouble shooting that is necessary for 

successful completion of the experimental aims. Furthermore, Dr. Smith will be responsible for 

the overall administration and coordination of the project. 

Mengxin Geng, Graduate Research Assistant, She (50% effort, 6 mo; year 1), will be working 

under the supervision of Dr. Smith. An effort of 50% is the maximum reportable effort for a 

graduate research assistant given their educational training. Mengxin is knowledgeable of 

techniques used isolating occidiofungin and analogs of occidiofungin. Her efforts, along with Dr. 

Smith, will be aimed at furthering the understanding of the bioactivity of each analogs and 

making the decision as to which analog has the best properties to move forward with preclinical 

development. 

MATERIALS AND SUPPLIES

Costs for disposable supplies, chemicals, media, and chromatography supplies are based prior 

experience from past practices. Additional costs are being budgeted for peptide synthesis. 

EQUIPMENT

No equipment is being requested 

TRAVEL

No travel funds are being requested. 

FEDERALLY NEGOTIATED INDIRECT COST RATE 

Texas A&M recovers under Modified Total Direct Cost basis with an indirect cost recovery of 

48.5%.

 

Contact PD/PI: Smith, James Leif 

Budget Justification Attachment Page 27
	
Contact PD/PI: Smith, James Leif 

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303 . Received Date:

2016-09-03T22:03:46.000-04:00

RESEARCH & RELATED BUDGET - Cumulative Budget

Totals ($)

Section A, Senior/Key Person

Section B, Other Personnel

Total Number Other Personnel 1

Total Salary, Wages and Fringe Benefits

(A+B)

Section C, Equipment

Section D, Travel

1. Domestic

2. Foreign

Section E, Participant/Trainee Support

Costs

1. Tuition/Fees/Health Insurance

2. Stipends

3. Travel

4. Subsistence

5. Other

6. Number of Participants/Trainees

Section F, Other Direct Costs

1. Materials and Supplies

2. Publication Costs 0.00

3. Consultant Services 0.00

4. ADP/Computer Services 0.00

5. Subawards/Consortium/Contractual

Costs

0.00

6. Equipment or Facility Rental/User

Fees

7. Alterations and Renovations 0.00

8. Other 1

9. Other 2

10. Other 3

Section G, Direct Costs

(A thru F)

Section H, Indirect Costs

Section I, Total Direct and Indirect Costs

(G + H)

Section J, Fee

 Page 28 
Contact PD/PI: Smith, James Leif 

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303. Received Date:

2016-09-03T22:03:46.000-04:00

 

Total Direct Costs less Consortium F&A

 

NIH policy (NOT-OD-05-004) allows applicants to exclude consortium/contractual F&A costs when determining if an application falls at or beneath any applicable direct cost limit. When a direct

cost limit is specified in an FOA, the following table can be used to determine if your application falls within that limit. 

Category Budget

Period 1

Budget

Period 2

Budget

Period 3

Budget

Period 4

Budget

Period 5

TOTALS

Total Direct Costs less Consortium F&A 0 0 0 0

 Page 29 
Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303. Received Date:

2016-09-03T22:03:46.000-04:00

SBIR/STTR Information

OMB Number: 4040-0001

Expiration date: 06/30/2016

Program Type (select only one)*

❍ SBIR ● STTR ❍ Both  (See agency-specific instructions to determine whether a particular agency allows a single submission for

both SBIR and STTR)

SBIR/STTR Type (select only one)*

● Phase I ❍ Phase II ❍ Fast-Track (See agency-specific instructions to determine whether a particular agency participates in FastTrack)

Questions 1-7 must be completed by all SBIR and STTR Applicants:

1a. Do you certify that at the time of award your organization will meet the eligibility criteria for a

small business as defined in the funding opportunity announcement?*

● Yes ❍ No

1b. Anticipated Number of personnel to be employed at your organization at the time of award.* 5

2. Does this application include subcontracts with Federal laboratories or any other Federal

Government agencies?*

❍ Yes ● No

If yes, insert the names of the Federal laboratories/agencies:*

3. Are you located in a HUBZone? To find out if your business is in a HUBZone, use the mapping

utility provided by the Small Business Administration at its web site: http://www.sba.gov *

❍ Yes ● No

4. Will all research and development on the project be performed in its entirety in the United

States?*

● Yes ❍ No

If no, provide an explanation in an attached file. Explanation:*

5. Has the applicant and/or Program Director/Principal Investigator submitted proposals for

essentially equivalent work under other Federal program solicitations or received other Federal

awards for essentially equivalent work?*

❍ Yes ● No

If yes, insert the names of the other Federal agencies:*

6. Disclosure Permission Statement: If this application does not result in an award, is the

Government permitted to disclose the title of your proposed project, and the name, address,

telephone number and e-mail address of the official signing for the applicant organization, to

organizations that may be interested in contacting you for further information (e.g., possible

collaborations, investment)?*

● Yes ❍ No

7. Commercialization Plan: If you are submitting a Phase II or Phase I/Phase II Fast-Track Application, include a Commercialization

Plan in accordance with the agency announcement and/or agency-specific instructions.*

Attach File:*

Contact PD/PI: Smith, James Leif 

 Page 30
	
Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303. Received Date:

2016-09-03T22:03:46.000-04:00

SBIR/STTR Information

OMB Number: 4040-0001

Expiration date: 06/30/2016

SBIR-Specific Questions:

Questions 8 and 9 apply only to SBIR applications. If you are submitting ONLY an STTR application, leave questions 8 and 9 blank and

proceed to question 10.

8. Have you received SBIR Phase II awards from the Federal Government? If yes, provide a

company commercialization history in accordance with agency-specific instructions using this

attachment.*

❍ Yes ❍ No

Attach File:*

9. Will the Project Director/Principal Investigator have his/her primary employment with the small

business at the time of award?*

❍ Yes ❍ No

STTR-Specific Questions:

Questions 10 and 11 apply only to STTR applications. If you are submitting ONLY an SBIR application, leave questions 10 and 11

blank.

10. Please indicate whether the answer to BOTH of the following questions is TRUE:*

(1) Does the Project Director/Principal Investigator have a formal appointment or commitment either with the small business directly

(as an employee or a contractor) OR as an employee of the Research Institution, which in turn has made a commitment to the small

business through the STTR application process; AND

(2) Will the Project Director/Principal Investigator devote at least 10% effort to the proposed project?

● Yes ❍ No

11. In the joint research and development proposed in this project, does the small business

perform at least 40% of the work and the research institution named in the application perform at

least 30% of the work?*

● Yes ❍ No

Contact PD/PI: Smith, James Leif 

 Page 31
	
PHS 398 Cover Page Supplement

OMB Number: 0925-0001

Expiration Date: 10/31/2018

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303 . Received Date:

2016-09-03T22:03:46.000-04:00

1. Human Subjects Section

Clinical Trial? ❍ Yes ● No

*Agency-Defined Phase III Clinical Trial? ❍ Yes ❍ No

2. Vertebrate Animals Section

Are vertebrate animals euthanized? ❍ Yes ● No

If "Yes" to euthanasia

Is the method consistent with American Veterinary Medical Association (AVMA) guidelines?

❍ Yes ❍ No

If "No" to AVMA guidelines, describe method and proved scientific justification

3. *Program Income Section

*Is program income anticipated during the periods for which the grant support is requested?

❍ Yes ● No

If you checked "yes" above (indicating that program income is anticipated), then use the format below to reflect the amount and

source(s). Otherwise, leave this section blank.

*Budget Period *Anticipated Amount ($) *Source(s)

Contact PD/PI: Smith, James Leif 

 Page 32
	
PHS 398 Cover Page Supplement

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303 . Received Date:

2016-09-03T22:03:46.000-04:00

4. Human Embryonic Stem Cells Section

*Does the proposed project involve human embryonic stem cells? ❍ Yes ● No

If the proposed project involves human embryonic stem cells, list below the registration number of the specific cell line(s) from the

following list: http://grants.nih.gov/stem_cells/registry/current.htm. Or, if a specific stem cell line cannot be referenced at this time,

please check the box indicating that one from the registry will be used:

Specific stem cell line cannot be referenced at this time. One from the registry will be used.

Cell Line(s) (Example: 0004):

5. Inventions and Patents Section (RENEWAL)

*Inventions and Patents: ❍ Yes ❍ No

If the answer is "Yes" then please answer the following:

*Previously Reported: ❍ Yes ❍ No

6. Change of Investigator / Change of Institution Section

❏ Change of Project Director / Principal Investigator

Name of former Project Director / Principal Investigator

Prefix:

*First Name:

Middle Name:

*Last Name:

Suffix:

❏ Change of Grantee Institution

*Name of former institution:

Contact PD/PI: Smith, James Leif 

 Page 33
	
 

PHS 398 Research Plan

OMB Number: 0925-0001

Expiration Date: 10/31/2018

 

Tracking Number: GRANT12241216 Funding Opportunity Number: PA-16-303. Received Date:

2016-09-03T22:03:46.000-04:00

Introduction

1. Introduction to Application

(Resubmission and Revision)

Research Plan Section

2. Specific Aims 1243-specificaims.pdf

3. Research Strategy* 1244-researchstrategy.pdf

4. Progress Report Publication List

Human Subjects Section

5. Protection of Human Subjects

6. Data Safety Monitoring Plan

7. Inclusion of Women and Minorities

8. Inclusion of Children

Other Research Plan Section

9. Vertebrate Animals

10. Select Agent Research

11. Multiple PD/PI Leadership Plan

12. Consortium/Contractual Arrangements  

13. Letters of Support 1245-departmentletter.pdf

14. Resource Sharing Plan(s) 1246-ResourceSharingPlan.pdf

15. Authentication of Key Biological and/or

Chemical Resources

Appendix

16. Appendix

Contact PD/PI: Smith, James Leif 

 Page 34
	
RESEARCH PLAN 

Specific Aims 

Occidiofungins, isolated from Burkholderia contaminans MS14, are a newly discovered class of antifungals. 

From our structural characterization studies, occidiofungin was determined to have a unique chemical 

composition. These studies revealed four main analogs, occidiofungins A-D, and the presence of two distinct 

diastereomers. All analogs are composed of eight amino acids and a novel C18 fatty amino acid (NAA) 

containing a xylose sugar, and a 2,4- diaminobutyric acid (DABA). The structural analogs differ by an addition 

of oxygen to asparagine 1 (Asn1) forming a β-hydroxy asparagine 1 (BHN1) and by the addition of chlorine to 

β-hydroxy tyrosine 4 (BHY) forming 3-chloro β-hydroxy tyrosine 4 (chloro-BHY). So far, a mixture of 

occidiofungin A-D analogs show promise for developing a novel therapeutic option for treating life threatening 

fungal infection. There is a critical need to isolate and characterize the bioactivity and toxicity of each of these 

natural analogs, as well as semi-synthetically produced analogs. The potential to develop new clinically useful 

approaches to mitigate human susceptibility to infections caused by fungal pathogens like Candida albicans

will likely remain limited, unless we further understand the therapeutic potential for each of these compounds. 

Our long-term goal is to develop an alternative treatment option for serious fungal infections, in which 

currently available antifungals are failing too many people. Our objective in this application is to characterize 

the naturally produced and semi-synthetically made analogs of occidiofungin. Our central hypothesis is that 

one of these analogs has a superior set of qualities for preclinical development and that these analogs need to 

be evaluated to identify a lead compound. This hypothesis was based on our preliminary data showing a 

difference in the spectrum of activity for some of these structural analogs. The rationale for the proposed 

research is that a lead compound needs to be identified in order to ensure success with the required preclinical 

studies before we have our pre-IND meeting with the FDA. We propose the following aims: 

Objective: Develop a novel therapeutic approach to treat life-threatening fungal infections. The occidiofungin 

analogs in this application will be screened based on their bioactivity in the presence of serum and toxicity 

against a mouse cell line. A lead drug candidate for therapeutic development will be identified from this study. 

Specific Aim 1: Synthesize, engineer, and isolate structural analogs of occidiofungin. 

Given our structural characterization and understanding of occidiofungin biosynthesis, we are able to 

engineer the synthesis of natural analogs of occidiofungin. The disruption and overexpression of gene 

products in the biosynthetic pathway will provide means to produce a homogenous culture of analogs of 

interest. Furthermore, we propose to screen semi-synthetic analogs by modifying an available amine in 

the molecule. Lastly, we propose to evaluate the possibility of producing occidiofungins by solid phase 

peptide synthesis. These studies are aimed to expand our understanding of the bioactivity of the 

naturally occurring analogs, while simultaneously evaluating the utility of chemically synthesizing novel 

analogs. 

Specific Aim 2: Characterize the bioactivity of each structural analogs. 

Microorganisms do not normally expend additional energy unless there is a good reason. It is likely that 

each naturally produced analog has a distinct set of bioactivities and toxicity. Fundamentally, we hope 

to understand the structure activity relationships (SAR) of the different structural elements found within 

occidiofungins A-D and the semi-synthetic analogs. Towards this aim, the bioactivity of each 

occidiofungin analog shall be determined using several methods to evaluate the spectrum of activity, 

serum binding, and time-kill kinetics. Occidiofungin analogs shall also be tested for differences in their 

in vitro toxicity profile using a rat hepatoma (H4IIE) cell line. These studies will expand our 

understanding of the biological activity and toxicity of each occidiofungin analog. 

At the completion of these studies, it is our expectation that we will have identified a lead compound of 

occidiofungin that has the best attributes for preclinical testing. These results are expected to have an 

important positive impact because current antifungals have limitations in use and are failing a significant 

population of susceptible patients. Occidiofungin is rapidly fungicidal, which may improve the therapeutic 

outcome for these patients. We are well equipped with the knowledge and experience to successfully complete 

this proposal. 

 

Contact PD/PI: Smith, James Leif 

Specific Aims Page 35
	
Research Strategy 

(A) Significance 

Antifungals are very important for the treatment of fungal infections particularly in immunocompromised 

and organ transplant patients (1-11). There is an absolute need for an alternative antifungal treatment option in 

the clinic. Hence, the development of newer class of antifungals with different mechanism of action and 

antifungal spectrum is desperately needed. Occidiofungin is a unique natural product (Figure 1) that has 

demonstrated attributes that can potentially fill this need. We are currently working to optimize the production 

of occidiofungin in B. contaminans or heterologous system. In connection to these studies, we would like to 

propose further studies aimed at engineering the production of natural and semi-synthetic analogs of 

occidiofungin. A major obstacle is the separation of natural occidiofungin variants. It is possible to move 

forward with the clinical development of a mixture of defined occidiofungin analogs. However, it would be better 

to isolate each of these analogs and determine differences in bioactivity and toxicity. We propose to evaluate 

these activities by improving our isolation methods, but we are also proposing to engineer the biosynthetic 

pathway to produce the analogs of interest. This system will not only lead to the isolation of the desired 

product, but also a novel system for the production of a defined analog of occidiofungin. This information can 

be integrated into our current production and optimization studies. Following the completion of the proposed 

studies in this application, identification of the desired occidiofungin analog/s will be done along with an 

engineered system to promote the production of the desired analog/s. 

Global market for antifungal therapeutics (in humans) was 

11.8 billion dollars in 2013 and is expected to be 13.9 billion by 

2018 (1). The U.S. antifungal market in 2013 was 4.9 billion 

dollars and expected to grow to 5.5 billion dollars by 2018 (1). 

More than 60% of the antifungal market is for the treatment of 

life threatening infections, which is also the proposed 

application for occidiofungin. Fluconazole, belonging to the 

azole class of antifungals, has had over one billion dollars in 

annual sales, despite limitations in its uses. Our current 

findings suggest that occidiofungin is structurally (Figure 1) and 

functionally a unique antifungal (12, 13); it has a superior 

spectrum of activity and lower toxicity than the drugs currently 

used to treat serious fungal infections. Advantages of 

occidiofungin over currently used antifungals arise from its fungicidal activity and novel mechanism of action 

(14, 15) in conjunction with the minimal toxicity observed in an animal studies (16). Composition and methods 

of use patent for occidiofungin has been filed in the U.S (US 2011/0136729). Patent was filed on May 25, 

2010. PCT National Phase Applications have been filed in November 2011 for Japan, European Patent Office, 

China, and South Korea. These filing will help secure worldwide protection. We do not anticipate any problems 

with the issue of our patents. 

(B) Innovation

Current antifungals that are used to treat systemic infections only target membrane and cell wall integrity. 

Azoles and echinocandins are fungistatic and moderately fungicidal (10, 11, 17, 18), respectively. This often 

poses a problem for successful treatment, given that individuals with serious fungal infections are usually 

severely immunocompromised. Current antifungal treatments lead to abnormal liver function test and have 

limitations with respect to their spectra of activity and toxicities. Occidiofungin is fungicidal with a unique 

mechanism of action as it induces apoptosis in yeast cells (14, 15). Current mouse studies with occidiofungin 

shows no organ specific toxicity (16). The proposed research is innovative, in our opinion, as we will identify a 

lead occidiofungin based compound for developing a novel therapeutic to alleviate the healthcare burden 

associated with fungal infections. Engineering the biosynthetic pathway or developing a semi-synthetic route 

for producing pure analogs of occidiofungin will promote its development for treating serious fungal infections. 

Currently, we are working with a natural mixture of the major occidiofungin products that are not easily 

separable. Following successful completion of Aim I, we shall have purified fraction of all eight naturally 

occurring analogs of occidiofungin for future studies. Each of these bacterial strains, engineered to produce a 

 

Contact PD/PI: Smith, James Leif 

Research Strategy Page 36
	
defined analog of occidiofungin, can be utilized to produce the desired analog for drug development studies. 

We also propose to evaluate a semi-synthetic production approach for occidiofungin analogs. Identification of a 

lead compound is an important consideration that needs to be made before we start our new investigational 

drug studies (IND). It is our aim to put forward the best occidiofungin analog for preclinical studies. Successful 

completion of this study will provide a means to identify the lead compound that is most likely to succeed 

during clinical development. 

(C) Approach 

Introduction: 

There is a substantial need for an alternative drug treatment for serious fungal infections. Limitations of one 

or more of the currently used antifungal drugs include high recurrence of infection, high mortality rates, poor 

oral bioavailability, limitations in spectrum of activity, and liver toxicity. Mechanism of action studies with 

occidiofungin support our assertion that the novel molecule has a unique fungal target (15). All three major 

thresholds for developing a novel antifungal for clinical use have been met by the antifungal occidiofungin. 

First threshold is to have a unique chemical composition.

• Occidiofungin is a hybrid product of NRPS-PKS whose complete chemical composition has been determined. 

It is a 1200 Da cyclic glyco-lipopeptide (Figure 1) (12, 13). 

Second threshold is having a similar or better spectrum of activity as compared to amphotericin B and 

fluconazole. 

• Minimum inhibitory concentrations (MICs) of occidiofungin against Candida species are between 0.5 and 1.0 

μg/mL (14). 

• Occidiofungin retains its in vitro potency against Candida in the presence of 5% and 50% human serum with 

a minimum lethal concentration (MLC) of 2 and 4 μg/mL, respectively (14). 

• Time-kill experiments revealed that occidiofungin is rapidly fungicidal against Candida albicans(14). 

• Post-antifungal experiments, where occidiofungin was washed away from the media, still exhibited potent 

antifungal activity against Candida. These experiments suggest that occidiofungin has a strong interaction 

with its target (14). 

• Cryptococcus neoformans is insensitive to echinocandins, but is susceptible to occidiofungin at submicromolar concentrations. Antifungal activity of occidiofungin has been demonstrated against a wide array 

of fungi (13, 14). 

• Mechanism of action studies suggests that an alternate target exists for occidiofungin other than targeting 

ergosterol production, binding to ergosterol or inhibiting the 1,3-β-glucan synthase enzyme, which are the 

current therapeutic targets for treating fungal infections (14, 15). 

The third threshold is having a similar or better toxicity profile compared to amphotericin B and fluconazole. 

• Female B6C3F1 mice were used to assess the acute toxicological effects of occidiofungin. Mice were given 

occidiofungin up to 20 mg/kg body weight (single dose) or 2mg/kg body weight daily for 5 days by 

intraperitoneal injection. All mice survived these dosages. Variables evaluated included body weight, 

selected organ weights, clinical 

chemistry, clinical and anatomic 

pathology, and behavioral 

phenomena. Key effects included 

a transient irritation at the site of 

injection, and body weight 

reductions. There was a 

significant increase in the 

percentage of neutrophils in the 

blood and a decrease in thymus 

weight relative to body weight 

after a single dose, which is 

characteristic of a non-specific 

 

Contact PD/PI: Smith, James Leif 

Research Strategy Page 37
	
stress response. Adaptation seems to be rapid, because these effects were not observed after 5 daily 

doses. Histological sections did not exhibit organ specific toxicity in liver, lung, thymus, and kidney (16). 

• Occidiofungin has a long half-life following i.v. administration and has been shown to reduce mortality and 

fungal load in the kidneys of female BALB/C mice (Figure 2A and 2B). 

Justification: 

Occidiofungin, along with very few antifungal compounds, has met these three criteria, and therefore holds 

promise as a potential antifungal therapeutic agent. The current need towards clinical development is 

identifying the lead compound of occidiofungin for preclinical studies. The aims described in our application will 

enable our group to produce a defined analog of occidiofungin that can be further evaluated for differences in 

bioactivity and toxicity. This information is crucial as it will improve the success rate for developing 

occidiofungin as a new antifungal therapeutic. 

Objective: Produce structurally defined analogs of occidiofungin to identify a lead compound for preclinical 

studies. 

Specific Aim 1: Synthesize, engineer, and isolate 

structural analogs of occidiofungin. 

Preliminary Data for the Biosynthesis of Occidiofungin (12, 

19-21): 

Sequencing of the ocf gene cluster and the detailed 

structural characterization of occidiofungin provided an 

excellent opportunity to model the biosynthesis of 

occidiofungin (Figure 3). The ocf gene cluster encodes all 

the gene products required for the synthesis of 

occidiofungin (12). The order in which the modules 

function, so that they are in agreement with the structure 

are as follows: OcfJ-OcfI-OcfH-OcfF-OcfE-OcfD. The 

amino acid sequence of the cyclic peptide is Asn/βhydroxyasparagine (BHN1)-novel amino acid(NAA2)-Ser3- 

β-hydroxytyrosine (BHY4)-Diaminobutyric acid (DABA5)-

Gly6-Asn7-Ser8. The ocfG gene encodes a homolog of an 

enzyme, StaM of the A47934 cluster, known to be involved 

in the formation of BHY(12). It is likely that the enzyme is 

responsible for the β-hydroxylations of Tyr4 and Asn1. 

Given the presence of Asn and BHN at position 1, it is also 

possible that the hydroxylation of Asn by ocfG is inefficient, 

leading to a mixture of Asn and BHN residues at position 1. 

The C-terminal region of OcfD, is predicted to have a TE 

domain, which is important for the condensation reaction of Ser8 to Asn/BHN1, which terminates synthesis and 

forms the cyclic peptide. The ocfN gene also codes for a thioesterase that is involved in the cyclization of the 

peptide. The ocfK gene codes for a homolog of nonheme iron dioxygenases that can catalyze 

chlorinations(12). It is likely that this enzyme catalyzes the 3-chloro addition that is observed on BHY4 (12). 

There are more than eight different structural analogs of occidiofungin. Only some of the analogs have 

been successfully separated by chromatography. To date, the spectrum of activity, mechanism of action, and 

toxicity studies have been done using a mixture of four structural analogs (A-D). The structural analogs of 

occidiofungin are known to result from the presence or lack of a: β-hydroxyl group on asparagine 1 

(occidiofungins A and B), chlorine on BHY4 (occidiofungins C and D), or xylose on NAA2 (Figure 1). In 

addition, there are two diastereomers formed by two distinct cyclase thioesterases, OcfN and OcfD (21). Given 

the risk and cost associated with the development of new antimicrobial compounds, it is crucial to identify a 

specific analog or a well characterized combination of structural analogs that have the best antifungal 

properties for the treatment of systemic fungal infections. The production of said analogs or combination must 

be well regulated and reproducible towards scalability of the process for large scale production. 

 

Contact PD/PI: Smith, James Leif 

Research Strategy Page 38
	
We plan to isolate the products of each natural analog of occidiofungin via genetic modification and 

chromatography. We have previously shown that the biosynthetic pathway for occidiofungin is amenable to 

genetic modification enabling the directed synthesis of different structural analogs of occidiofungin (12, 21, 22). 

The disruption and over-expression of specified gene products in the biosynthetic pathway provides a specific 

bacterial strain that will produce a well characterized structural analogs of occidiofungin. Engineering of a strain 

that can produce a specific occidiofungin analog would also provide a pure starting material for determining 

activity differences, thus, promoting lead compound identification. In addition, we propose a semi-synthetic 

route by modifying a free amine in occidiofungin and by utilizing the OcfN thioesterase to cyclize a synthesized 

peptide. This approach may lead to new analogs of occidiofungin that may have different antifungal spectrum 

and or improved pharmacokinetic, pharmacodynamic properties. The combination of site directed modification 

and solid phase peptide synthesis (SPPS), as proposed in this application, will expand the structural repertoire 

of compounds that may have improved bioactivities. 

Research Strategy: 

Manipulating the producing organism to make each structural analog of occidiofungin is a practical 

approach as long as it is used in conjunction with the characterization of the structural analogs that can be 

isolated via chromatographic separation. We have the experience and molecular tools to produce the 

stereoisomer analogs and the individual β-hydroxylated and chlorinated analogs proposed below (12, 21, 22).

Production of the stereoisomers formed by the thioesterase OcfD and OcfN. We predicted that the 

thioesterase domain of OcfD and the thioesterase coded by ocfN were both required for cyclization of each 

distinct diastereomer. A nonpolar mutation was constructed in the open reading frame of wild-type ocfN by the 

insertion of a kanamycin resistance gene, nptII. The B. contaminans MS14 mutant (ocfN::nptII) produced only 

one of the diastereomers. NMR analysis revealed the loss of the stereoisomers formed by OcfN (5). The 

bioactivity of the OcfD diastereomer products was compared to the bioactivity of the purified wild-type 

occidiofungin analogs A-D containing both diastereomers. There was a two-fold decrease in activity for the 

OcfD diastereomer product against Candida spp. An observed two-fold decrease in activity for these analogs, 

given that they make up approximately half of the wild-type occidiofungin analogs, suggests that the activity of 

the OcfN diastereomer is four-fold more active against Candida spp. This data does support our hypothesis 

that the bacterium is making different analogs of occidiofungin to increase its spectrum of activity (5). Recently, 

the production of the OcfN diastereomer has also been accomplished following the same mutagenesis 

procedure described for MS14 mutant (ocfN::nptII). We are in the process of purifying enough of the MS14 

mutant (ocfD::nptII) product for bioactivity and NMR studies. 

Production of the occidiofungin analogs lacking xylose (∆Xyl). The B. contaminans MS14 mutant 

(ocfC::nptII) produces an analog that no longer has the xylose sugar attached to the novel amino acid (NAA2) 

(8). The bioactivity of the analogs lacking the xylose, which we call occidiofungin A-D(∆Xyl), has a similar 

bioactivity against Candida spp as the analogs containing the xylose (8). Therefore, the presence of the xylose 

sugar is not essential for antifungal activity. This is good news as we plan to synthesize new analogs by SPPS. 

We need to characterize occidiofungin A-D(∆Xyl) according to the experiments outlined in specific aim 2. We 

do see an increase in neutrophils in our animal studies following administration of occidiofungin containing the 

xylose sugar. We can also alleviate lethargy observed in mice at higher doses (5-10mg/mL) by administering 

the antihistamine cetirizine. Given that xylose is not normally present in animal systems, it may be responsible 

for triggering an innate immune response and the occidiofungin A-D(∆Xyl) analogs may minimize these 

observed effects. 

Production of the occidiofungin analogs AB or CD. Before embarking on the bioengineering of B. 

contaminans MS14 to produce individual analogs of occidiofungins A-D, we need to characterize the bioactivity 

differences of occidiofungins A-B and occidiofungins C-D. We have recently been able to separate these 

structural analogs by chromatography. Depending on the outcome of the spectrum of activity and toxicity 

studies using these fractions, we will determine the most beneficial structural analog to bioengineer. Production 

of mixed analogs A-B and C-D will be carried out by knocking out the halogenase ocfK or by overexpressing 

ocfK. The practical reason for this approach is that it should lead to a differential increase in the amount of the 

A-B product or C-D product expressed by the bacterium. The vector pMLS7 was constructed to overexpress 

genes in the Burkholderia cells (9) and successfully used by my group (1, 5, 8). To promote the halogenase 

activity, 0.1-1mM CaCl2 will also be supplemented into the media. This has been shown to be successful in 

 

Contact PD/PI: Smith, James Leif 

Research Strategy Page 39
	
other halogenated natural products (10-12). Once we show an increase in chlorination within our system, we 

can use this system to determine the halogenase’s specificity to other halides such as bromide and iodide. 

Production of synthetic analogs of occidiofungin. The free amino group on the 

DABA residue provides a region in which we can synthesize additional structural 

analogs (Figure 1). We have prepared alkyne NHS ester with > 90% yield for 

microscopy imaging studies using azide derivatized fluorescent dyes. In these 

studies, we have determined that occidiofungin is intracellularly localized. We will 

investigate additional structural modifications within this region that may 

positively impact bioactivity. We have recently finished the Marphey's 

derivitization studies on occidiofungin to determine the chirality of each amino 

acid. Based on this data, and supported by the knowledge of known epimerase 

domains within the NRPS enzymes, the stereochemistry of the individual amino 

acids are: (L)Asn1-(L)NAA2-(L)Ser3-(D)BHY4-(D)DABA5-Gly6-(L)Asn7-(D)Ser8. 

Given the predicted increase in bioactivity of the OcfN cyclase thioesterase 

product (5), we will use this enzyme for the last cyclization step for our SPPS 

peptides with a C-terminal N-acetylcysteamine (SNAC) group. This approach will 

enable us to substitute amino acids and will provide a detailed understanding of the "structure activity 

relationship" of this molecule. We have expressed and purified the OcfN cyclase thioesterase (Figure 4). The 

SPPS peptides will be purchased from a commercial peptide supplier (Peptide Elephants). The first peptide will 

contain a β-homo alanine at the NAA2 position to test the activity of the OcfN cyclase. This substitution will 

maintain the peptide backbone structure for optimizing the enzymatic cyclase activity. We believe that NAA2 is 

important for penetrating the fungal plasma membrane. Synthesis of NAA2 is simplified with the knowledge 

that the xylose is not needed for activity (22). Other functional groups will be explored that may have more 

desirable attributes while still promoting the peptide's entry into the cell. We will need to synthesize some of the 

desired β-amino acids for NAA2 position, but many of the Fmoc and Boc labeled β-amino acids are available 

through Sigma Aldrich. 

Potential Problems and Alternative Approaches: One potential problem that can occur is that the insertion of 

nptII in the ocfD thioesterase domain, may interfere with the function of other modules within the protein, 

resulting in a loss of occidiofungin biosynthesis. An alternative approach is to use the suicide vector 

pJQ200mp18 with a Kmr cassette insertion in the plasmid region of the gentamicin resistance gene (gtmR) 

(pJQ200mp18:Kmr). The 800 bp fragment described above will be amplified with flanking BamHI restriction 

sites and cloned into pGEM-T Easy Vector System I. The conserved serine in the GXSXG active site motif of 

the thioesterase will be replaced by an alanine. Primers with 5’ overlapping regions will be used to change the 

serine codon to an alanine by circle PCR mutagenesis. The PCR product will be introduced into E. coli and the 

bacterium will form the plasmid using the overlapping 5’ regions introduced by the primers. The desired 

plasmid will be isolated from E. coli grown on LB-Amp plates for selection. If circle PCR doesn’t work, two-step 

PCR will be used to clone the mutated product. Plasmids will be sequenced to confirm the mutation. The 

product will be digested with BamHI and cloned into pJQ200mp18:Kmr. Integration of the plasmid into the ocfD

gene will be selected for using kanamycin. The sacB/sucrose counterselection system will be used to identify 

the revertants (loss of plasmid). Half of these revertants should contain the mutation. PCR and sequencing 

will be used to identify the mutation introduced into B. contaminans MS14. If mutating the active site of the 

thioesterase does not yield the desired product, another approach will be used to make the Asn1 analogs. 

Disruption of the hydroxylase gene, ocfG, should prevent the synthesis of both BHN and BHY. This mutation 

may prevent the biosynthesis of occidiofungin, in the event that BHY is required for biosynthesis. The activity 

can presumably be restored by supplementing BHY into the media as has been reported for the production of 

balhimycin (23). 

Expected outcomes. We will have isolated natural structural analogs of occidiofungin upon completion of Aim 

1. The outlined approaches will provide a unique basis for not only testing the bioactivity of each analog, but 

provide a means to specifically produce each compound. The compounds isolated in this study will be 

evaluated for its bioactivity and toxicity for identifying new therapeutic agents for the treatment of invasive 

fungal infections in patients who are intolerant or not responding to other therapies. 

Specific Aim 2: Characterize the bioactivity of each structural analog. 

 

Contact PD/PI: Smith, James Leif 

Research Strategy Page 40
	
We have the necessary experience to characterize the bioactivity of the occidiofungin analogs (12, 14, 15, 19-

21). 

Research Strategy: 

In vitro susceptibility testing. MICs for Aspergillus, Penicillium, Cryptococcus, Microsporum, Pythium, 

Trichophyton, and Candida spp. will be determined by using Clinical Laboratory Standards Institute (CLSI) 

method M27-A3 and M38-A2. MIC endpoints for occidiofungin are then determined by visual inspection and 

will be based on the wells that have no visible growth (an optically clear well) after 24 and 48 hours of 

incubation. Susceptibility testing will be done in duplicates. DMSO containing no antifungal agent will be used 

as a negative control and Amphotericin B as a positive control. 

Determine the effects of protein binding on the activity of occidiofungin. The most direct approach to 

determine the effect of protein binding on the antifungal activity of occidiofungin is to test the compound in the 

presence of serum. Susceptibility testing, as described above, will be performed in duplicate according to the 

CLSI M27-A3 method in RPMI or YPD growth medium in the presence of 5% and 50% (vol/vol) human sera 

(Sigma Aldrich, St. Louis, MO). This will provide information as to the amount of unbound antifungal 

compound that is present in blood. This information is also important for future formulations for efficacy studies 

in an animal model. Given the turbidity of 50% serum, 50μL of cell suspension in each well of the microtiter 

well will be plated to determine the minimum lethal concentration (MLC). 

Determine the kinetics of activity and the post antifungal effects on Candida spp. These experiments 

provide important information about the activity of the occidiofungin analogs. These studies will determine the 

rate of fungicidal activity. The post antifungal effect (PAFE) experiments will determine the relative effect 

occidiofungin has on cells exposed for a short time period. Time-kill assays are a measurement of CFUs 

following the addition of the antifungal to the yeast. We will observe the kinetics over a 24 hour period following 

addition of a suspension of C. albicans or C. glabrata to a culture tube containing varying concentrations of 

occidiofungin. The suspension is prepared from colonies that are removed from a fresh (24 hour old) YPD 

plate and suspended in sterile water to an O.D.530 of 0.13. The suspension is then diluted ten-fold by adding 

1mL to 9mL of RPMI 1640 containing the desired concentration of the antifungal compound and incubated at 

35°C with agitation. At time 0, 2, 4, 8, 24 hours, 100μL of cell suspension is drawn from the culture and serially 

diluted to obtain the CFUs. PAFE experiments are performed in a similar manner. Following a 1-hour exposure 

to occidiofungin, the tubes are spun down at 5000 rpm for ten minutes, washed three times, and resuspended 

in fresh, warm RPMI 1640 media. CFU are measured at 2, 4, 8, and 24 hours. These experiments will be 

conducted on all newly isolated analogs of occidiofungin. Amphotericin B will be used as a control for 

comparison between data sets. 

In vitro toxicity screen. Cytotoxicity will be evaluated by monitoring membrane integrity and mitochondrial 

function. Cellular ATP assay, MTT and Glutathione S-transferase assays will be performed as previously 

reported by our group (16), using a rat hepatoma (H4IIE) cell line. Amphotericin B and rotenone will be used 

as a control. 

Potential Problems and Alternative Approaches: We have expertise with the assays outlined in this aim. They 

are widely used in the antimicrobial research community. There may need to be some modifications to these 

protocols as problems arise that do not conform to these assays. For instance, several strains of S. cerevisiae

in my lab will not grow in RPMI 1640 used for MICs and time-kill assays and YPD broth has to be used instead. 

We expect similar situations to arise as we perform our spectrum of activity screening and will make 

modifications to protocols as needed. 

Expected outcomes. Aim 2 will enable us to determine the importance of these structural modifications 

relative to their spectrum of activity, time-kill kinetics and toxicity. These results are important in that they will 

enable our group to identify a lead analog with the most promising attributes for successfully developing a new 

antifungal therapeutic. 

Timeline: These aims will identify lead occidiofungin analog/s, which is necessary before initiating our pre-IND 

meeting with the FDA. The completion of this study will coincide with the completion of our optimized 

production and purification studies and provide us with the knowledge needed to move occidiofungin into 

clinical studies. Experiment outline in Aim 1 are expected to take approximately one year, while the studies in 

Aim 2 can be done as the analogs become available. 

 

Contact PD/PI: Smith, James Leif 

Research Strategy Page 41
	
References 

1. Anonymous. 2014. Antifungal Drugs: Technologies and Global Markets. BCC Research June:1-164. 

2. Cuenca-Estrella M, Rodriguez D, Almirante B, Morgan J, Planes AM, Almela M, Mensa J, 

Sanchez F, Ayats J, Gimenez M, Salvado M, Warnock DW, Pahissa A, Rodriguez-Tudela JL. 

2005. In vitro susceptibilities of bloodstream isolates of Candida species to six antifungal agents: 

results from a population-based active surveillance programme, Barcelona, Spain, 2002-2003. J 

Antimicrob Chemoth 55:194-199. 

3. Dauber JH, Paradis IL, Dummer JS. 1990. Infectious complications in pulmonary allograft recipients. 

Clin Chest Med 11:291-308. 

4. Dummer JS, Montero CG, Griffith BP, Hardesty RL, Paradis IL, Ho M. 1986. Infections in heart-lung 

transplant recipients. Transplantation 41:725-729. 

5. Edmond MB, Wallace SE, McClish DK, Pfaller MA, Jones RN, Wenzel RP. 1999. Nosocomial 

bloodstream infections in United States hospitals: a three-year analysis. Clin Infect Dis 29:239-244. 

6. Hibberd PL, Rubin RH. 1994. Clinical aspects of fungal infection in organ transplant recipients. Clin 

Infect Dis 19 Suppl 1:S33-S40. 

7. Kavanagh K. 2007. New Insights in Medical Mycology. Springer, New York, NY 

8. Kubak BM. 2002. Fungal infection in lung transplantation. Transplant Infect Dis 4 Suppl 3:24-31. 

9. Morgan J, Meltzer MI, Plikaytis BD, Sofair AN, Huie-White S, Wilcox S, Harrison LH, Seaberg EC, 

Hajjeh RA, Teutsch SM. 2005. Excess mortality, hospital stay, and cost due to candidemia: a casecontrol study using data from population-based candidemia surveillance. Infect Contr Hosp Epidem 

26:540-547. 

10. Naeger-Murphy N, Pile JC. 2009. Clinical Indications for Newer Antifungal Agents. J Hosp Med 4:102-

111. 

11. Schaenman JM, Rosso F, Austin JM, Baron EJ, Gamberg P, Miller J, Oyer PE, Robbins RC, 

Montoya JG. 2009. Trends in invasive disease due to Candida species following heart and lung 

transplantation. Transplant Infect Dis 11:112-121. 

12. Gu G, Smith L, Liu A, Lu S-E. 2011. Genetic and biochemical map for the biosynthesis of 

occidiofungin, an antifungal produced by Burkholderia contaminans strain MS14. Appl Environ 

Microbiol 77:6189-6198. 

13. Lu S-E, Novak J, Austin FW, Gu G, Ellis D, Kirk M, Wilson-Stanford S, Tonelli M, Smith L. 2009. 

Occidiofungin, a unique antifungal glycopeptide produced by a strain of Burkholderia contaminans. 

Biochemistry 48:8312. 

14. Ellis D, Gosai J, Emrick C, Heintz R, Romans L, Gordon D, Lu S, Austin F, Smith L. 2012. 

Occidiofungin’s Chemical Stability and In vitro Potency Against Candida species. Antimicrob Agents 

Chemother 56:765-769. 

15. Emrick D, Ravichandran A, Gosai J, Lu S, Gordon DM, Smith L. 2013. The antifungal occidiofungin 

triggers an apoptotic mechanism of cell death in yeast. J Nat Prod 76:829-838. 

16. Wei T, Cooley J, Austin F, Lu S, Smith L, Pruett S. 2012. Pre-clinical Toxicological Evaluation of 

Occidiofungin, a Unique Glyco-lipopeptide Antifungal. Inter J Toxicol 31:326-336. 

17. Charlier C, Hart E, Lefort A, Ribaud P, Dromer F, Denning DW, Lortholary O. 2006. Fluconazole for 

the management of invasive candidiasis: where do we stand after 15 years? J Antimicrob Chemother 

57:384-410. 

18. Pfaller MA, Diekema DJ, Jones RN, Sader HS, Fluit AC, Hollis RJ, Messer SA. 2001. International 

surveillance of bloodstream infections due to Candida species: frequency of occurrence and in vitro 

susceptibilities to fluconazole, ravuconazole, and voriconazole of isolates collected from 1997 through 

1999 in the SENTRY antimicrobial surveillance program. J Clin Microbiol 39:3254-3259. 

19. Gu G, Wang N, Chaney N, Smith L, Lu S-E. 2009. AmbR1 is a key transcriptional regulator for 

production of antifungal activity of Burkholderia contaminans strain MS14. FEMS Microbiol Lett 

297:54-60. 

20. Gu GY, Smith L, Wang N, Wang H, Lu SE. 2009. Biosynthesis of an antifungal oligopeptide in 

Burkholderia contaminans strain MS14. Biochem Biophys Res Commun 380:328-332. 

21. Ravichandran A, Gu G, Escano J, Lu S-E, Smith L. 2013. The presence of two cyclase thioesterases 

expands the conformational freedom of the cyclic Peptide occidiofungin. J Nat Prod 76:150-156. 

 

Contact PD/PI: Smith, James Leif 

References Cited Page 42
	
22. Chen K-C, Ravichandran A, Guerrero A, Deng P, Baird SM, Smith L, Lu S-E. 2013. The 

Burkholderia contaminans MS14 ocfC gene encodes a xylosyltransferase for production of the 

antifungal occidiofungin. Appl Environ Microbiol 79:2899-2905. 

23. Puk O, Bischoff D, Kittel C, Pelzer S, Weist S, Stegmann E, Sussmuth RD, Wohlleben W. 2004. 

Biosynthesis of chloro-beta-hydroxytyrosine, a nonproteinogenic amino acid of the peptidic backbone of 

glycopeptide antibiotics. J Bacteriol 186:6093-6100. 

 

Contact PD/PI: Smith, James Leif 

References Cited Page 43
	
 

Contact PD/PI: Smith, James Leif 

COLLEGE OF SCIENCE

Department of Biology

Butler Hall 100 

3258 TAMU 

College Station, Texas 77843-3258 

Tel. 979.845.7747 Fax. 979.845.2891 

www.bio.tamu.edu 

30 August 2016 

To Whom It May Concern: 

This letter is to confirm that Dr. James L. Smith is a full-time, tenured faculty member in the 

Department of Biology at Texas A&M University where he holds the rank of Associate 

Professor. Dr. Smith’s current research involves drug development and structure-activity 

relationship studies of antimicrobial compounds. His excellent past productivity indicates that 

he will be successful in achieving his research goals. He has the department’s full support for 

his application titled, "Lead Compound Discovery from Engineered Analogs of Occidiofungin". 

Sincerely, 

Thomas D. McKnight 

Professor and Head of Biology 

Letters of Support Page 44
	
Resource Sharing Plan 

Data Sharing Plan

Nature of the materials to be shared includes, but is not limited to, experimental techniques, 

information about experimental materials, methods employed for data interpretation, raw data 

and our conclusions drawn from the data. Given the nature of the study, intellectual property 

decisions will need to be made prior to the release of information. However, there are no 

complicating factors that would prevent the investigator from sharing information after the filing 

of a provisional application. Data and materials will be shared in the following manners: 

A. Attendance at Scientific Meetings 

Local 

Members of the PI laboratory will present data acquired from this proposal to the local research 

community within the state of Texas. Opportunities exist for personnel to present their research 

accomplishments in poster format at regional Symposiums held on Texas A&M campus. These 

events are open to the entire University community. Investigators will disseminate research 

findings by giving research seminars at local universities including Rice and University of Texas. 

Regional 

Research results obtained with the support of this grant will be the basis of poster and oral 

presentations to be made at yearly regional meetings. Personnel will be encouraged to attend 

these events. These regional meetings are excellent opportunities for networking and the 

exchange of ideas and research materials. Example meeting includes the Texas Branch 

American Society for Microbiology. 

National/International 

To reach large numbers of the scientific community, data derived during the execution of this 

proposal will be presented at national scientific meetings. Example meetings include those held 

by the American Society for Cell Biology, American Society for Biochemistry and Molecular 

Biology, and the American Society for Microbiology Candida and IACACC Meeting. 

These meetings are well attended and a large number of international labs participate providing 

an opportunity for our research findings to reach a broader audience. 

B. Peer-reviewed Publications 

Data acquired during this project will be written up for publication in appropriate peer-reviewed 

journals. All results will be published in a timely manner. 

 

Contact PD/PI: Smith, James Leif 

Resource Sharing Plan(s) Page 45