Attachment 1 - Chemistry Software Support SOW.pdf

Statement of Work (SOW) Chemistry Software

INTRODUCTION

PURPOSE OF CONTRACT

The purpose of this contract will be to procure ready to install chemistry software to support the National Institute of Neurological Disorders and Stroke (NINDS) Preclinical Screening Platform for Pain (PSPP) and Epilepsy Therapy Screening Program (ETSP) programs. Under this purchase order, the contractor will provide chemistry software ready to integrate with NIH systems the day contract is awarded that will help in drawing, storing, and searching the chemical structures of small or large compounds. The chemistry software will also support searches of the structures on the Public Access to Neuroactive & Anticonvulsant Chemical Evaluations (PANAChE) database.

The new contract for chemistry software should continue to provide all the similar existing chemistry software functionalities and support.

BACKGROUND

The National Institutes of Health (NIH) is the nation’s leading medical research agency and the primary Federal agency whose mission is to seek fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to enhance health, lengthen life, and reduce illness and disability, conducting, supporting, and making medical discoveries that improve people’s health and save lives.

The mission of the NINDS ETSP is to facilitate the discovery of new therapeutic agents that address the unmet medical needs in epilepsy. Historically, the ETSP has focused on identifying symptomatic treatments for seizure disorders, but recent adjustments have moved the program to focus on addressing drug resistant epilepsy, disease prevention and modification. The program provides opportunities for researchers from academia and industry in the U.S. and abroad to submit compounds for screening in a battery of rodent epilepsy and seizure models. These tests are performed at a contract facility based at the University of Utah on a blinded and confidential basis and at no cost to the ETSP participants. The NINDS ETSP staff reports test results to participants and provides advice on next steps for promising compounds. Since its establishment in 1975, the program has made important contributions to the development of several FDA-approved drugs for epilepsy, including felbamate (Felbatol), topirimate (Topamax), lacosamide (Vimpat), retigabine (Potiga), cannabidiol (Epidiolex) and cenobamate (Xcopri) (https://www.ninds.nih.gov/current-research/focus-disorders/epilepsy-research/epilepsy-therapy-screening-program-etsp).

The PSPP facilitates the identification of potential non-opioid, non-addictive treatments (small molecules, biologics, natural products, or devices) for acute and chronic pain conditions. PSPP accepts assets for evaluation from academic researchers, industry, including small businesses, and government institutions worldwide. Under NINDS direction, preclinical evaluation of accepted assets is performed by contract facilities on a blinded and confidential basis and at no cost to the PSPP participants (https://www.ninds.nih.gov/current-research/trans-agency-activities/ninds-role-heal-initiative/preclinical-screening-platform-pain-pspp).

SCOPE OF WORK

https://www.ninds.nih.gov/glossary?title=NINDS https://www.ninds.nih.gov/current-research/focus-disorders/epilepsy-research/epilepsy-therapy-screening-program-etsp https://www.ninds.nih.gov/current-research/focus-disorders/epilepsy-research/epilepsy-therapy-screening-program-etsp

Independently and not as an agent of the Government, the contract awardee shall furnish all the necessary services, qualified personnel, materials, equipment, and facilities, not otherwise provided by the Government as needed to perform the actions outlined in this SOW.

The scope of this procurement is to acquire desktop and web chemistry software licenses for up to 15 users to be used in continuing efforts of the NINDS Preclinical Screening Platform for Pain (PSPP) and Epilepsy Therapy Screening Program (ETSP). The desktop and web chemistry software are vital for the continuous operation of the ETSP and PSPP web-based applications including those which are offered to the public by the NINDS ETSP and PSPP programs. The current contract (HHSN271201800630P) provides the required tools below for the PSPP and ETSP program to function smoothly.

Required Features for Chemistry Software:

Chemistry Requirements:

1. Chem Structure Drawing

a. Structure to name (IUPAC)

b. Name to structure

c. Recognize common names

d. Atom drawing

e. Periodic Table

f. Calculate the Formula and Mass of selected structures or fragments

g. Charge

h. Isotope

i. Enhanced stereo notation

j. Bond (single / double/ triple) query properties

k. Chain Drawing

l. Setting absolute stereo (Chiral)

m. Atom lists/NOT lists

n. R-group labels, definition, logic

o. Coordinate bond from multi-atom group

p. Valence check

q. Aromatization

r. Mapping

s. Structure Checker

t. Structure display (wireframe, ball & stick, space fill)

u. R/S and E/Z stereo notation

v. Biomolecule display

2. Elemental Analysis

a. Exact and nominal mass, molecular weight and atom count

b. Elemental composition

c. Molecular formula

d. Molecular composition

3. NMR predictor

a. Predict 13C and 1H NMR spectra

4. Solubility

a. pH-dependent solubility

b. Solubility in water

5. Partitioning

a. LogP

b. LogD

6. Protonation

a. Calculation of pKa values along with pH dependent distribution.

Software Requirements:

• Provide chemistry software web interface to draw chemistry structures, template based

Please specify the underlying tool used to develop

• Chemistry software web interface (Draw / View / Search / Update/ Export / Import structures) shall provide support to be integrated with ASP.NET MVC5 web applications.

• Chemistry software web interface (Draw / View / Search / Update/ Export / Import structures) shall provide support to be integrated with ASP.NET Core web applications.

• Chemistry desktop structure editor software shall integrate with ETSP desktop application

(ADDSII) which is running on .NET Framework 4. Chemistry desktop structure editor software shall be able to Draw / View / Search / Update / Export and Import structures.

• Chemistry software must operate in a Windows environment and have no dependency on any other operating environment (e.g., Linux environment).

• Chemistry software shall provide following features.

Conversion from structure to Image.

Check given structure for errors if any.

Web Interface shall be able to upload and represent chemical structures from various data types, including but not limited to, SMILES strings, InChI strings, MRV, SD files, and Mol files, among others. The web interface shall display stereoselective features of chemical structures, such as chiral centers and stereoisomers.

Shall offer structure-based searching capacity, including the ability to search and easily sort by substructure and structural similarities.

Export structure to Excel.

Provide technical documentation with examples.

• Chemistry software shall support Microsoft SQL Server 2019, 2022 database and any subsequent latest releases.

• Chemistry software shall provide user-friendly Application Program Interfaces (APIs) for the above chemistry functionality.

• Software, including all data needed shall operate independently and be housed within the NIH firewall to draw / import / export structure and used to calculate various chemistry data points.

• Software must be compliant with section 508.

MAINTENANCE AND SUPPORT

Prompt customer support shall be available as needed when issues occur, and resolution will be available on a reasonably agreed upon time by the NINDS COR and contractor.

The contractor will be responsible for maintenance and support of the tool as follows:

Technical consultation services may be required to support specific user issues or unmet needs. Latest updates and features should also be included. Chemistry software should function within the boundaries and restrictions of NINDS IT Security changes. Chemistry software should function even after any operating system updates, and if there are issues with the chemistry software after operating system or any other software updates, technical support must trouble shoot and resolve the issue.

OPTIONAL SUPPORT

To assist the NINDS, should a software issue arise that can’t be solved with standard support provided in the base license price, the NINDS will request Optional Support that can be exercised at the Contracting Officer’s discretion. Should NINDS have a technical problem that requires Optional Support, this option will be exercised, and the support will start as soon as the contractor is notified of option exercise. The Contractor should provide a quote for additional, higher-level support and describe how it would be provided.

OPTIONAL REQUIREMENT: ADME

If available, the Contractor shall provide an optional tool that can estimate the predicted absorption, distribution, metabolism, and excretion (ADME) properties of a compound for the base and option periods.

PERIOD OF PERFORMANCE

Base: September 30, 2024 – September 29, 2025 Option Year 1: September 30, 2025 – September 29, 2026 Option Year 2: September 30, 2026 – September 29, 2027 Option Year 3: September 30, 2027 – September 29, 2028 Option Year 4: September 30, 2028 – September 29, 2029

PLACE OF PERFORMANCE

All contractor work will occur at their own work facilities and communication with NIH staff will occur over email, phone, and videoconference.

GOVERNMENT FURNISHED EQUIPMENT (GFE)

The government will not provide any GFE for this requirement. The contractor will supply all staff and equipment to conduct all activities in this SOW.

INFORMATION SECURITY

The contractor will work with NINDS to comply with NINDS Information Security Program Requirements.

DATA RIGHTS

All data developed in relation to this requirement shall be owned with unlimited rights by the Government.

SECTION 508 COMPLIANCE AND ACCESSIBILITY

Applications and products shall be in compliance with the stipulations of Section 508 of the Rehabilitation Act, 29 U.S.C. § 794d, as amended.